tag:blogger.com,1999:blog-89592270898154637042024-03-13T14:30:21.167+08:00Kevin's GATTACA WorldMy Weblog on Bioinformatics, Genome Science and Next Generation SequencingUnknownnoreply@blogger.comBlogger1132125tag:blogger.com,1999:blog-8959227089815463704.post-54686403121817646092021-10-05T18:10:00.006+08:002021-10-05T18:10:49.588+08:00HGVS nomenclature<p> Was recently asked about HGVS nomenclature reporting. The fun thing about biology is that there's going to be exceptions to the rule or some shenanigans that you didn't expect when setting out a rule. </p><p>"The Human Genome Variation Society (HGVS) provides standardized recommendations for describing human sequence variants, which are widely accepted in the scientific community, especially in the practice of clinical molecular pathology.1 Use of the HGVS nomenclature system is a de facto recommendation for clinical reporting of sequence variants.2, 3 Being a core component of the clinical report, incorrect HGVS nomenclature can have a negative impact on patient care, such as misdiagnosis or clinical trial ineligibility. HGVS nomenclature has been traditionally computed manually by pathologists from Sanger sequencing electropherograms. However, manually computing HGVS nomenclature is time consuming, complex, and error prone, particularly with insertion and deletion (indel) variants, resulting in inconsistencies across laboratories."</p><p><a href="https://www.sciencedirect.com/science/article/pii/S1525157817306220" target="_blank">Source</a>:Clinical Implementation and Validation of Automated Human Genome Variation Society (HGVS) Nomenclature System for Next-Generation Sequencing–Based Assays for Cancer</p><p><span style="-webkit-text-stroke-width: 0px; background-color: white; color: #1c1d1e; display: inline !important; float: none; font-family: "Open Sans", sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-decoration-thickness: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;">In the 25th Anniversary Special Issue of<span> </span></span><i style="-webkit-text-stroke-width: 0px; background-color: white; box-sizing: border-box; color: #1c1d1e; font-family: "Open Sans", sans-serif; font-size: 16px; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-decoration-thickness: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;">Human Mutation</i><span style="-webkit-text-stroke-width: 0px; background-color: white; color: #1c1d1e; display: inline !important; float: none; font-family: "Open Sans", sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-decoration-thickness: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;">, Den Dunnen et al. (</span><span style="-webkit-text-stroke-width: 0px; background-color: white; box-sizing: border-box; color: #1c1d1e; font-family: "Open Sans", sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-decoration-thickness: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;"><a class="bibLink tab-link" data-tab="pane-pcw-references" href="https://onlinelibrary.wiley.com/doi/full/10.1002/humu.22978#humu22978-bib-0001" id="humu22978-bib-0001R" style="background-color: transparent; box-sizing: border-box; color: black; cursor: pointer; display: inline; font-size: inherit; font-weight: 600; text-decoration: underline;">2016</a></span><span style="-webkit-text-stroke-width: 0px; background-color: white; color: #1c1d1e; display: inline !important; float: none; font-family: "Open Sans", sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-decoration-thickness: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;">) publish an update of the Human Genome Variation Society (HGVS) recommendations for the description of sequence variants (</span><a class="linkBehavior" href="http://www.hgvs.org/varnomen" style="-webkit-text-stroke-width: 0px; background-color: white; box-sizing: border-box; color: #005274; cursor: pointer; display: inline; font-family: "Open Sans", sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 600; letter-spacing: normal; orphans: 2; text-align: start; text-decoration: underline; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;">http://www.HGVS.org/varnomen</a><span style="-webkit-text-stroke-width: 0px; background-color: white; color: #1c1d1e; display: inline !important; float: none; font-family: "Open Sans", sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-decoration-thickness: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;">). One of the issues discussed is how widespread HGVS nomenclature is used and, when used, whether published variant descriptions correctly follow the recommendations. An<span> </span></span><i style="-webkit-text-stroke-width: 0px; background-color: white; box-sizing: border-box; color: #1c1d1e; font-family: "Open Sans", sans-serif; font-size: 16px; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-decoration-thickness: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;">EGFR</i><span style="-webkit-text-stroke-width: 0px; background-color: white; color: #1c1d1e; display: inline !important; float: none; font-family: "Open Sans", sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-decoration-thickness: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;"><span> </span>(OMIM# 131550) lung cancer testing scheme assessed in January 2016 by the United Kingdom National External Quality Assessment Scheme (UK NEQAS) for Molecular Genetics demonstrates the current variability in the use and interpretation of the HGVS guidelines by diagnostic laboratories based across the globe.</span></p><p><span style="-webkit-text-stroke-width: 0px; background-color: white; color: #1c1d1e; display: inline !important; float: none; font-family: "Open Sans", sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-decoration-thickness: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;">Source: <a href="https://onlinelibrary.wiley.com/doi/full/10.1002/humu.22978" target="_blank">HGVS Nomenclature in Practice: An Example from the United Kingdom National External Quality Assessment Scheme</a> </span> </p><p> </p><p>Shall explore this tool </p><p><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6282708/" target="_blank">hgvs: A Python package for manipulating sequence variants using HGVS nomenclature: 2018 Update</a> <br /></p><p>https://github.com/biocommons/hgvs <br /></p>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-8959227089815463704.post-46931680089182791312021-09-28T19:02:00.008+08:002021-09-28T19:02:35.838+08:00Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers | Nature Methods <p style="font-family: Calibri, sans-serif; font-size: 11pt; margin-left: 0in; margin-right: 0in;"> Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers | Nature Methods </p><div style="-webkit-text-stroke-width: 0px; background-color: white; border: 0px; color: black; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; font-stretch: inherit; font-style: normal; font-variant-caps: normal; font-variant-east-asian: inherit; font-variant-ligatures: normal; font-variant-numeric: inherit; font-weight: 400; letter-spacing: normal; line-height: inherit; margin: 0px; orphans: 2; padding: 0px; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-decoration-thickness: initial; text-indent: 0px; text-transform: none; vertical-align: baseline; white-space: normal; widows: 2; word-spacing: 0px;"><p style="font-family: Calibri, sans-serif; font-size: 11pt; margin-left: 0in; margin-right: 0in;"> </p><div style="border: 0px; color: inherit; font-family: Calibri, sans-serif; font-size: 11pt; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; line-height: inherit; margin: 0px 0in; padding: 0px; vertical-align: baseline;"><a href="https://www.nature.com/articles/s41592-021-01254-9" id="LPlnk" style="border: 0px; font: inherit; margin: 0px; padding: 0px; vertical-align: baseline;">https://www.nature.com/articles/s41592-021-01254-9</a><br /></div><div class="_Entity _EType_OWALinkPreview _EId_OWALinkPreview _EReadonly_1" contenteditable="false" style="border: 0px; color: inherit; font: inherit; margin: 0px; padding: 0px; vertical-align: baseline;"><div class="LPBorder602641" id="LPBorder_GTaHR0cHM6Ly93d3cubmF0dXJlLmNvbS9hcnRpY2xlcy9zNDE1OTItMDIxLTAxMjU0LTk." style="border: 0px; color: inherit; font: inherit; margin: 16px 0px; max-width: 800px; min-width: 424px; padding: 0px; position: relative; vertical-align: baseline; width: 424px;"><table id="LPContainer602641" role="presentation" style="border-color: rgb(200, 200, 200); border-radius: 2px; border-style: solid; border-width: 1px; font: inherit; padding: 12px 36px 12px 12px; width: 442.3px;"><tbody><tr style="border-spacing: 0px;" valign="top"><td><div id="LPImageContainer602641" style="border: 0px; color: inherit; font: inherit; height: 159.066px; margin: 0px 12px 0px 0px; overflow: hidden; padding: 0px; position: relative; vertical-align: baseline; width: 240px;"><a href="https://www.nature.com/articles/s41592-021-01254-9" id="LPImageAnchor602641" style="border: 0px; font: inherit; margin: 0px; padding: 0px; vertical-align: baseline;" target="_blank"><img alt="" height="159" id="LPThumbnailImageId602641" src="https://media.springernature.com/m685/springer-static/image/art%3A10.1038%2Fs41592-021-01254-9/MediaObjects/41592_2021_1254_Fig1_HTML.png" style="border: 0px; color: inherit; display: block; font: inherit; margin: 0px; padding: 0px; vertical-align: baseline;" width="240" /></a></div></td><td style="width: 131.5px;"><div id="LPTitle602641" style="border: 0px; color: inherit; font-family: wf_segoe-ui_light, "Segoe UI Light", "Segoe WP Light", "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif; font-size: 21px; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-weight: 300; line-height: inherit; margin: 0px 8px 12px 0px; padding: 0px; vertical-align: baseline;"><a href="https://www.nature.com/articles/s41592-021-01254-9" id="LPUrlAnchor602641" style="border: 0px; color: var(--themePrimary); font: inherit; margin: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" target="_blank">Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers | Nature Methods</a></div><div id="LPDescription602641" style="border: 0px; color: #666666; font-family: wf_segoe-ui_normal, "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif; font-size: 14px; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; line-height: inherit; margin: 0px 8px 12px 0px; max-height: 100px; overflow: hidden; padding: 0px; vertical-align: baseline;">The rapid growth of high-throughput technologies has transformed biomedical research. With the increasing amount and complexity of data, scalability and reproducibility have become essential not ...</div><div id="LPMetadata602641" style="border: 0px; color: #a6a6a6; font-family: wf_segoe-ui_normal, "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif; font-size: 14px; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-weight: 400; line-height: inherit; margin: 0px; padding: 0px; vertical-align: baseline;">www.nature.com</div></td></tr></tbody></table><div class="_2M3vYXiVaXB9t5mk-HJrJj" id="LPCloseButtonContainer602641" role="button" style="border: 0px; color: inherit; cursor: pointer; font: inherit; height: 32px; margin: 0px; padding: 0px; pointer-events: all; position: absolute; right: 4px; text-align: center; top: 4px; vertical-align: baseline; width: 32px;" tabindex="0" title="Remove link preview"><i aria-hidden="true" class="X4fFibeUI1qc3DQiCmjWf root-100" data-icon-name="Cancel" id="LPCloseButton602641" style="-webkit-font-smoothing: antialiased; color: var(--neutralSecondary); display: block; font-family: controlIcons; font-size: 17px; font-style: normal; font-weight: 300; line-height: 32px; margin: auto; pointer-events: none; position: relative; speak: none;"></i></div><div class="_2M3vYXiVaXB9t5mk-HJrJj" id="LPCloseButtonContainer602641" role="button" style="border: 0px; color: inherit; cursor: pointer; font: inherit; height: 32px; margin: 0px; padding: 0px; pointer-events: all; position: absolute; right: 4px; text-align: center; top: 4px; vertical-align: baseline; width: 32px;" tabindex="0" title="Remove link preview"><i aria-hidden="true" class="X4fFibeUI1qc3DQiCmjWf root-100" data-icon-name="Cancel" id="LPCloseButton602641" style="-webkit-font-smoothing: antialiased; color: var(--neutralSecondary); display: block; font-family: controlIcons; font-size: 17px; font-style: normal; font-weight: 300; line-height: 32px; margin: auto; pointer-events: none; position: relative; speak: none;"></i></div></div></div><br /><a href="https://github.com/GoekeLab/bioinformatics-workflows" id="LPlnk" style="border: 0px; font: inherit; margin: 0px; padding: 0px; vertical-align: baseline;">https://github.com/GoekeLab/bioinformatics-workflows</a> <br /><div class="_Entity _EType_OWALinkPreview _EId_OWALinkPreview_1 _EReadonly_1" contenteditable="false" style="border: 0px; color: inherit; font: inherit; margin: 0px; padding: 0px; vertical-align: baseline;"><div class="LPBorder265406" id="LPBorder_GTaHR0cHM6Ly9naXRodWIuY29tL0dvZWtlTGFiL2Jpb2luZm9ybWF0aWNzLXdvcmtmbG93cw.." style="border: 0px; color: inherit; font: inherit; margin: 16px 0px; max-width: 800px; min-width: 424px; padding: 0px; position: relative; vertical-align: baseline; width: 424px;"><table id="LPContainer265406" role="presentation" style="border-color: rgb(200, 200, 200); border-radius: 2px; border-style: solid; border-width: 1px; font: inherit; padding: 12px 36px 12px 12px; width: 546.438px;"><tbody><tr style="border-spacing: 0px;" valign="top"><td><div id="LPImageContainer265406" style="border: 0px; color: inherit; font: inherit; height: 120px; margin: 0px 12px 0px 0px; overflow: hidden; padding: 0px; position: relative; vertical-align: baseline; width: 240px;"><a href="https://github.com/GoekeLab/bioinformatics-workflows" id="LPImageAnchor265406" style="border: 0px; font: inherit; margin: 0px; padding: 0px; vertical-align: baseline;" target="_blank"><img alt="" height="120" id="LPThumbnailImageId265406" src="https://opengraph.githubassets.com/093ef7e91a623feeb42613b890b1fca8383e9b3a1f2a27e8c79c4f76ffaadf72/GoekeLab/bioinformatics-workflows" style="border: 0px; color: inherit; display: block; font: inherit; margin: 0px; padding: 0px; vertical-align: baseline;" width="240" /></a></div></td><td style="width: 235.637px;"><div id="LPTitle265406" style="border: 0px; color: inherit; font-family: wf_segoe-ui_light, "Segoe UI Light", "Segoe WP Light", "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif; font-size: 21px; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-weight: 300; line-height: inherit; margin: 0px 8px 12px 0px; padding: 0px; vertical-align: baseline;"><a href="https://github.com/GoekeLab/bioinformatics-workflows" id="LPUrlAnchor265406" style="border: 0px; color: var(--themePrimary); font: inherit; margin: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" target="_blank">GitHub - GoekeLab/bioinformatics-workflows: minimal example implementations for bioinformatics workflow managers</a></div><div id="LPDescription265406" style="border: 0px; color: #666666; font-family: wf_segoe-ui_normal, "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif; font-size: 14px; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; line-height: inherit; margin: 0px 8px 12px 0px; max-height: 100px; overflow: hidden; padding: 0px; vertical-align: baseline;">Workflow managers provide an easy and intuitive way to simplify pipeline development. Here we provide basic proof-of-concept implementations for selected workflow managers. The analysis workflow is based on a small portion of an RNA-seq pipeline, using fastqc for quality controls and salmon for ...</div><div id="LPMetadata265406" style="border: 0px; color: #a6a6a6; font-family: wf_segoe-ui_normal, "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif; font-size: 14px; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-weight: 400; line-height: inherit; margin: 0px; padding: 0px; vertical-align: baseline;">github.com</div></td></tr></tbody></table><div class="_2M3vYXiVaXB9t5mk-HJrJj" id="LPCloseButtonContainer265406" role="button" style="border: 0px; color: inherit; cursor: pointer; font: inherit; height: 32px; margin: 0px; padding: 0px; pointer-events: all; position: absolute; right: 4px; text-align: center; top: 4px; vertical-align: baseline; width: 32px;" tabindex="0" title="Remove link preview"><i aria-hidden="true" class="X4fFibeUI1qc3DQiCmjWf root-100" data-icon-name="Cancel" id="LPCloseButton265406" style="-webkit-font-smoothing: antialiased; color: var(--neutralSecondary); display: block; font-family: controlIcons; font-size: 17px; font-style: normal; font-weight: 300; line-height: 32px; margin: auto; pointer-events: none; position: relative; speak: none;"></i></div><div class="_2M3vYXiVaXB9t5mk-HJrJj" id="LPCloseButtonContainer265406" role="button" style="border: 0px; color: inherit; cursor: pointer; font: inherit; height: 32px; margin: 0px; padding: 0px; pointer-events: all; position: absolute; right: 4px; text-align: center; top: 4px; vertical-align: baseline; width: 32px;" tabindex="0" title="Remove link preview"><i aria-hidden="true" class="X4fFibeUI1qc3DQiCmjWf root-100" data-icon-name="Cancel" id="LPCloseButton265406" style="-webkit-font-smoothing: antialiased; color: var(--neutralSecondary); display: block; font-family: controlIcons; font-size: 17px; font-style: normal; font-weight: 300; line-height: 32px; margin: auto; pointer-events: none; position: relative; speak: none;"></i></div></div></div></div><div style="-webkit-text-stroke-width: 0px; border: 0px; color: black; font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; font-size: 14px; font-stretch: inherit; font-style: normal; font-variant-caps: normal; font-variant-east-asian: inherit; font-variant-ligatures: normal; font-variant-numeric: inherit; font-weight: 400; letter-spacing: normal; line-height: inherit; margin: 0px; orphans: 2; padding: 0px; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-decoration-thickness: initial; text-indent: 0px; text-transform: none; vertical-align: baseline; white-space: normal; widows: 2; word-spacing: 0px;"><br class="Apple-interchange-newline" /><br /></div>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-8959227089815463704.post-76831684518557921172021-09-27T17:46:00.002+08:002021-09-27T17:46:49.635+08:00Orientation Bias artifect <p> <a href="https://gatk.broadinstitute.org/hc/en-us/community/posts/360075017111-strand-bias-and-orientation-bias">strand bias and orientation bias – GATK (broadinstitute.org)</a></p><p>"</p><p style="-webkit-text-stroke-width: 0px; background-color: white; box-sizing: border-box; color: black; font-family: Montserrat, -apple-system, BlinkMacSystemFont, "Segoe UI", Helvetica, Arial, sans-serif; font-size: 14px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; margin-top: 0px; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-decoration-thickness: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;">The read orientation artifact, also known as the orientation bias artifact, arises due to a chemical change in the nucleotide during library prep that results in, for example, G base-paring with A. This kind of artifact has a clear signature (e.g. C to A SNP that occurs predominantly for the middle C in the DNA sequence CCG), and it’s singlestranded in nature. Downstream, this artifact manifests as low allele fraction SNPs whose evidence for the alt allele consists almost entirely F1R2 reads or F2R1 reads. A read pair is F1R2 (forward 1st, reverse 2nd) if the sequence of bases in Read 1 maps to the forward strand of the reference (F1), and the sequence of Read 2 to the reverse strand<br style="box-sizing: border-box;" />of the reference (R2). F2R1 is defined similarly</p><p style="-webkit-text-stroke-width: 0px; background-color: white; box-sizing: border-box; color: black; font-family: Montserrat, -apple-system, BlinkMacSystemFont, "Segoe UI", Helvetica, Arial, sans-serif; font-size: 14px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; margin-top: 0px; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-decoration-thickness: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;"> </p><p style="-webkit-text-stroke-width: 0px; background-color: white; box-sizing: border-box; color: black; font-family: Montserrat, -apple-system, BlinkMacSystemFont, "Segoe UI", Helvetica, Arial, sans-serif; font-size: 14px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; margin-top: 0px; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-decoration-thickness: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;">if someone has read the dragonbioit used guide in illumina, it just mentioned orientation bias, ignore the strand bias.</p><p style="-webkit-text-stroke-width: 0px; background-color: white; box-sizing: border-box; color: black; font-family: Montserrat, -apple-system, BlinkMacSystemFont, "Segoe UI", Helvetica, Arial, sans-serif; font-size: 14px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; margin-top: 0px; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-decoration-thickness: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;">" <br /></p><p> </p>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-8959227089815463704.post-45455176206387836742021-09-17T02:23:00.001+08:002021-09-17T02:24:50.935+08:00Benchmarking variants and comparing truth sets: List of useful tools and publications<p></p><p style="-webkit-text-stroke-width: 0px; background-color: white; box-sizing: inherit; color: #333333; font-family: sans-serif; font-size: 14px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; line-height: 1.4285em; margin: 0px 0px 1em; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-decoration-thickness: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;">Just realised that other than <a href="https://vcftools.github.io/perl_module.html#vcf-compare">vcf-compare</a> and <a href="https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html">bedtools intersect </a></p><p style="-webkit-text-stroke-width: 0px; background-color: white; box-sizing: inherit; color: #333333; font-family: sans-serif; font-size: 14px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; line-height: 1.4285em; margin: 0px 0px 1em; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-decoration-thickness: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;">there's other options <br /></p><p style="-webkit-text-stroke-width: 0px; background-color: white; box-sizing: inherit; color: #333333; font-family: sans-serif; font-size: 14px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; line-height: 1.4285em; margin: 0px 0px 1em; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-decoration-thickness: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;"> </p><p style="-webkit-text-stroke-width: 0px; background-color: white; box-sizing: inherit; color: #333333; font-family: sans-serif; font-size: 14px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; line-height: 1.4285em; margin: 0px 0px 1em; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-decoration-thickness: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;"><a href="https://github.com/RealTimeGenomics/rtg-tools" rel="nofollow" style="background-color: transparent; box-sizing: inherit; color: #4183c4; padding: 0px; text-decoration: none;">https://github.com/RealTimeGenomics/rtg-tools</a></p><p style="-webkit-text-stroke-width: 0px; background-color: white; box-sizing: inherit; color: #333333; font-family: sans-serif; font-size: 14px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; line-height: 1.4285em; margin: 0px; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-decoration-thickness: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;"><a href="https://github.com/Illumina/hap.py" rel="nofollow" style="background-color: transparent; box-sizing: inherit; color: #4183c4; padding: 0px; text-decoration: none;">https://github.com/Illumina/hap.py</a></p><p style="-webkit-text-stroke-width: 0px; background-color: white; box-sizing: inherit; color: #333333; font-family: sans-serif; font-size: 14px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; line-height: 1.4285em; margin: 0px; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-decoration-thickness: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;"> </p><p>Also there's actually new variant callers .. <br /></p><p><span style="-webkit-text-stroke-width: 0px; background-color: white; color: #333333; display: inline !important; float: none; font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Oxygen-Sans, Ubuntu, Cantarell, "Helvetica Neue", sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-decoration-thickness: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;">Molina-Mora, J.A., Solano-Vargas, M. <a href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-03926-3#citeas">Set-theory based benchmarking of three different variant callers for targeted sequencing</a>.<span> </span></span><i style="-webkit-text-stroke-width: 0px; background-color: white; box-sizing: inherit; color: #333333; font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Oxygen-Sans, Ubuntu, Cantarell, "Helvetica Neue", sans-serif; font-size: 16px; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-decoration-thickness: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;">BMC Bioinformatics</i><span style="-webkit-text-stroke-width: 0px; background-color: white; color: #333333; display: inline !important; float: none; font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Oxygen-Sans, Ubuntu, Cantarell, "Helvetica Neue", sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-decoration-thickness: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;"><span> </span></span><b style="-webkit-text-stroke-width: 0px; background-color: white; box-sizing: inherit; color: #333333; font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Oxygen-Sans, Ubuntu, Cantarell, "Helvetica Neue", sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: bolder; letter-spacing: normal; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-decoration-thickness: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;">22,<span> </span></b><span style="-webkit-text-stroke-width: 0px; background-color: white; color: #333333; display: inline !important; float: none; font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Oxygen-Sans, Ubuntu, Cantarell, "Helvetica Neue", sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-decoration-thickness: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;">20 (2021). https://doi.org/10.1186/s12859-020-03926-3</span></p><p><span style="-webkit-text-stroke-width: 0px; background-color: white; color: #333333; display: inline !important; float: none; font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Oxygen-Sans, Ubuntu, Cantarell, "Helvetica Neue", sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-decoration-thickness: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;"> </span></p><p><span style="-webkit-text-stroke-width: 0px; background-color: white; color: #333333; display: inline !important; float: none; font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Oxygen-Sans, Ubuntu, Cantarell, "Helvetica Neue", sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-decoration-thickness: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;">Krishnan, V., Utiramerur, S., Ng, Z.<span> </span></span><i style="-webkit-text-stroke-width: 0px; background-color: white; box-sizing: inherit; color: #333333; font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Oxygen-Sans, Ubuntu, Cantarell, "Helvetica Neue", sans-serif; font-size: 16px; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-decoration-thickness: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;">et al.</i><span style="-webkit-text-stroke-width: 0px; background-color: white; color: #333333; display: inline !important; float: none; font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Oxygen-Sans, Ubuntu, Cantarell, "Helvetica Neue", sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-decoration-thickness: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;"><span> </span><a href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-03934-3#citeas">Benchmarking workflows to assess performance and suitability of germline variant calling pipelines in clinical diagnostic assays</a>.<span> </span></span><i style="-webkit-text-stroke-width: 0px; background-color: white; box-sizing: inherit; color: #333333; font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Oxygen-Sans, Ubuntu, Cantarell, "Helvetica Neue", sans-serif; font-size: 16px; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-decoration-thickness: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;">BMC Bioinformatics</i><span style="-webkit-text-stroke-width: 0px; background-color: white; color: #333333; display: inline !important; float: none; font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Oxygen-Sans, Ubuntu, Cantarell, "Helvetica Neue", sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-decoration-thickness: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;"><span> </span></span><b style="-webkit-text-stroke-width: 0px; background-color: white; box-sizing: inherit; color: #333333; font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Oxygen-Sans, Ubuntu, Cantarell, "Helvetica Neue", sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: bolder; letter-spacing: normal; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-decoration-thickness: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;">22,<span> </span></b><span style="-webkit-text-stroke-width: 0px; background-color: white; color: #333333; display: inline !important; float: none; font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Oxygen-Sans, Ubuntu, Cantarell, "Helvetica Neue", sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-decoration-thickness: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;">85 (2021). https://doi.org/10.1186/s12859-020-03934-3</span></p><h3 class="c-article-supplementary__title u-h3" style="-webkit-text-stroke-width: 0px; background-color: white; box-sizing: inherit; color: #1b3051; font-family: Europa, "Trebuchet MS"; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 700; letter-spacing: normal; line-height: 1.5; margin: 0px 0px 8px; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-decoration-thickness: initial; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;"><span style="font-size: small;"><a class="print-link" data-supp-info-image="" data-test="supp-info-link" data-track-action="view supplementary info" data-track-label="link" data-track="click" href="https://static-content.springer.com/esm/art%3A10.1186%2Fs12859-020-03934-3/MediaObjects/12859_2020_3934_MOESM23_ESM.py" style="background-color: transparent; box-sizing: inherit; color: #004b83; text-decoration-skip-ink: auto; text-decoration: none; word-break: break-word;"><b style="box-sizing: inherit; font-weight: bolder;">Additional file 23: File 3</b></a></span></h3><div class="c-article-supplementary__description" data-component="thumbnail-container" style="-webkit-text-stroke-width: 0px; background-color: white; box-sizing: inherit; color: #333333; font-family: Georgia, Palatino, serif; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; margin: 0px; padding: 0px; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-decoration-thickness: initial; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;"><p style="box-sizing: inherit; margin: 0px; padding: 0px;"><span style="font-size: small;">. verify_variants.py</span></p></div><p><span style="-webkit-text-stroke-width: 0px; background-color: white; color: #303030; display: inline !important; float: none; font-family: arial, helvetica, clean, sans-serif; font-size: 13px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: left; text-decoration-color: initial; text-decoration-style: initial; text-decoration-thickness: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;"> </span></p><p><span style="-webkit-text-stroke-width: 0px; background-color: white; color: #303030; display: inline !important; float: none; font-family: arial, helvetica, clean, sans-serif; font-size: 13px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: left; text-decoration-color: initial; text-decoration-style: initial; text-decoration-thickness: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;"> </span></p><p><span style="-webkit-text-stroke-width: 0px; background-color: white; color: #303030; display: inline !important; float: none; font-family: arial, helvetica, clean, sans-serif; font-size: 13px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: left; text-decoration-color: initial; text-decoration-style: initial; text-decoration-thickness: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;">Zook, Justin M et al. “<a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6500473/">An open resource for accurately benchmarking small variant and reference calls.</a>”<span> </span></span><i style="-webkit-text-stroke-width: 0px; background-color: white; color: #303030; font-family: arial, helvetica, clean, sans-serif; font-size: 13px; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: left; text-decoration-color: initial; text-decoration-style: initial; text-decoration-thickness: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;">Nature biotechnology</i><span style="-webkit-text-stroke-width: 0px; background-color: white; color: #303030; display: inline !important; float: none; font-family: arial, helvetica, clean, sans-serif; font-size: 13px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: left; text-decoration-color: initial; text-decoration-style: initial; text-decoration-thickness: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;"><span> </span>vol. 37,5 (2019): 561-566. doi:10.1038/s41587-019-0074-6</span></p><p></p><p><br /></p><p><br /></p><p class="f4 mt-3" style="-webkit-text-stroke-width: 0px; background-color: white; box-sizing: border-box; color: #24292f; font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Helvetica, Arial, sans-serif, "Apple Color Emoji", "Segoe UI Emoji"; font-size: 16px !important; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; margin-bottom: 10px; margin-top: 16px !important; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-decoration-thickness: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;">Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`</p><div class="mt-3 d-flex flex-items-center" style="-webkit-text-stroke-width: 0px; align-items: center !important; background-color: white; box-sizing: border-box; color: #24292f; display: flex !important; font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Helvetica, Arial, sans-serif, "Apple Color Emoji", "Segoe UI Emoji"; font-size: 14px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; margin-top: 16px !important; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-decoration-thickness: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;"><svg aria-hidden="true" class="octicon octicon-link flex-shrink-0 mr-2" data-view-component="true" height="16" viewbox="0 0 16 16" width="16"><path d="M7.775 3.275a.75.75 0 001.06 1.06l1.25-1.25a2 2 0 112.83 2.83l-2.5 2.5a2 2 0 01-2.83 0 .75.75 0 00-1.06 1.06 3.5 3.5 0 004.95 0l2.5-2.5a3.5 3.5 0 00-4.95-4.95l-1.25 1.25zm-4.69 9.64a2 2 0 010-2.83l2.5-2.5a2 2 0 012.83 0 .75.75 0 001.06-1.06 3.5 3.5 0 00-4.95 0l-2.5 2.5a3.5 3.5 0 004.95 4.95l1.25-1.25a.75.75 0 00-1.06-1.06l-1.25 1.25a2 2 0 01-2.83 0z" fill-rule="evenodd"></path></svg><span class="flex-auto min-width-0 css-truncate css-truncate-target width-fit" style="box-sizing: border-box; display: inline-block; flex: 1 1 auto !important; max-width: 125px; min-width: 0px !important; overflow: hidden; text-overflow: ellipsis; vertical-align: top; white-space: nowrap;"><a class="text-bold" href="https://hgvs.readthedocs.io/" rel="noopener noreferrer" role="link" style="background-color: transparent; box-sizing: border-box; color: var(--color-accent-fg); font-weight: 600 !important; text-decoration: none;" target="_blank" title="https://hgvs.readthedocs.io/">hgvs.readthedocs.io/</a></span></div><p><br /></p><p><br /></p><ul class="articles-list" id="similar-articles-list" style="-webkit-text-stroke-width: 0px; background-color: white; box-sizing: inherit; color: #212121; display: block; font-family: BlinkMacSystemFont, -apple-system, "Segoe UI", Roboto, Oxygen, Ubuntu, Cantarell, "Fira Sans", "Droid Sans", "Helvetica Neue", sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; line-height: 1.5; list-style: none; margin: 1.2rem 0px; orphans: 2; padding: 0px; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-decoration-thickness: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;"><li class="full-docsum" style="box-sizing: inherit; display: list-item; line-height: 2.4rem; margin: 0px 0px 1.2rem; padding: 0px; position: relative;"><div class="docsum-content" style="box-sizing: inherit; display: inline;"><span style="font-size: small;"><a class="docsum-title" data-ga-action="30129167" data-ga-category="similar_article" data-ga-label="" href="https://pubmed.ncbi.nlm.nih.gov/30129167/" style="background-color: transparent; box-sizing: inherit; color: #0071bc; display: inline-block; line-height: 2.4rem; margin: 0px; outline-offset: 0px; overflow-wrap: break-word; text-decoration: none;">hgvs: A Python package for manipulating sequence variants using HGVS nomenclature: 2018 Update.</a></span><div class="docsum-citation full-citation" style="box-sizing: inherit; color: #4d8055; line-height: 2.4rem;"><span style="font-size: small;"><span class="docsum-authors full-authors" style="box-sizing: inherit; color: #212121; display: block;">Wang M, Callenberg KM, Dalgleish R, Fedtsov A, Fox NK, Freeman PJ, Jacobs KB, Kaleta P, McMurry AJ, Prlić A, Rajaraman V, Hart RK.</span><span class="docsum-journal-citation full-journal-citation" style="box-sizing: inherit; display: block;">Hum Mutat. 2018 Dec;39(12):1803-1813. doi: 10.1002/humu.23615. Epub 2018 Sep 5.</span><span class="citation-part" style="box-sizing: inherit; display: inline-block;">PMID:<span> </span><span class="docsum-pmid" style="box-sizing: inherit;">30129167</span></span><span> </span><span class="free-resources spaced-citation-item citation-part" style="box-sizing: inherit; color: #c05600; display: inline-block; font-weight: 600; padding-left: 2.4rem;">Free PMC article.</span></span></div><div class="docsum-citation full-citation" style="box-sizing: inherit; color: #4d8055; font-size: 1.4rem; line-height: 2.4rem;"><ul class="articles-list" id="similar-articles-list" style="-webkit-text-stroke-width: 0px; background-color: white; box-sizing: inherit; color: #212121; display: block; font-family: BlinkMacSystemFont, -apple-system, "Segoe UI", Roboto, Oxygen, Ubuntu, Cantarell, "Fira Sans", "Droid Sans", "Helvetica Neue", sans-serif; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; line-height: 1.5; list-style: outside none none; margin: 1.2rem 0px; padding: 0px; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-decoration-thickness: initial; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;"><li class="full-docsum" style="box-sizing: inherit; display: list-item; line-height: 2.4rem; margin: 0px 0px 1.2rem; padding: 0px; position: relative;"><div class="docsum-content" style="box-sizing: inherit; display: inline;"><span style="font-size: small;"><a class="docsum-title" data-ga-action="27367167" data-ga-category="similar_article" data-ga-label="" href="https://pubmed.ncbi.nlm.nih.gov/27367167/" style="background-color: transparent; box-sizing: inherit; color: #0071bc; display: inline-block; line-height: 2.4rem; margin: 0px; outline-offset: 0px; overflow-wrap: break-word; text-decoration: none;">Sequence Variant Descriptions: HGVS Nomenclature and Mutalyzer.</a></span><div class="docsum-citation full-citation" style="box-sizing: inherit; color: #4d8055; line-height: 2.4rem;"><span style="font-size: small;"><span class="docsum-authors full-authors" style="box-sizing: inherit; color: #212121; display: block;">den Dunnen JT.</span><span class="docsum-journal-citation full-journal-citation" style="box-sizing: inherit; display: block;">Curr Protoc Hum Genet. 2016 Jul 1;90:7.13.1-7.13.19. doi: 10.1002/cphg.2.</span><span class="citation-part" style="box-sizing: inherit; display: inline-block;">PMID:<span> </span><span class="docsum-pmid" style="box-sizing: inherit;">27367167</span></span></span></div></div></li></ul><span class="free-resources spaced-citation-item citation-part" style="box-sizing: inherit; color: #c05600; display: inline-block; font-weight: 600; padding-left: 2.4rem;"> </span></div></div></li></ul><ul class="articles-list" id="similar-articles-list" style="-webkit-text-stroke-width: 0px; background-color: white; box-sizing: inherit; color: #212121; display: block; font-family: BlinkMacSystemFont, -apple-system, "Segoe UI", Roboto, Oxygen, Ubuntu, Cantarell, "Fira Sans", "Droid Sans", "Helvetica Neue", sans-serif; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; line-height: 1.5; list-style: outside none none; margin: 1.2rem 0px; padding: 0px; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-decoration-thickness: initial; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;"><li class="full-docsum" style="box-sizing: inherit; display: list-item; line-height: 2.4rem; margin: 0px 0px 1.2rem; padding: 0px; position: relative;"><div class="docsum-content" style="box-sizing: inherit; display: inline;"><span style="font-size: small;"><a class="docsum-title" data-ga-action="25273102" data-ga-category="similar_article" data-ga-label="" href="https://pubmed.ncbi.nlm.nih.gov/25273102/" style="background-color: transparent; box-sizing: inherit; color: #0071bc; display: inline-block; line-height: 2.4rem; margin: 0px; outline-offset: 0px; overflow-wrap: break-word; text-decoration: none;">A Python package for parsing, validating, mapping and formatting sequence variants using HGVS nomenclature.</a></span><div class="docsum-citation full-citation" style="box-sizing: inherit; color: #4d8055; line-height: 2.4rem;"><span style="font-size: small;"><span class="docsum-authors full-authors" style="box-sizing: inherit; color: #212121; display: block;">Hart RK, Rico R, Hare E, Garcia J, Westbrook J, Fusaro VA.</span><span class="docsum-journal-citation full-journal-citation" style="box-sizing: inherit; display: block;">Bioinformatics. 2015 Jan 15;31(2):268-70. doi: 10.1093/bioinformatics/btu630. Epub 2014 Sep 30.</span><span class="citation-part" style="box-sizing: inherit; display: inline-block;">PMID:<span> </span><span class="docsum-pmid" style="box-sizing: inherit;">25273102</span></span><span> </span><span class="free-resources spaced-citation-item citation-part" style="box-sizing: inherit; color: #c05600; display: inline-block; font-weight: 600; padding-left: 2.4rem;">Free PMC article.</span></span></div></div></li><li class="full-docsum" style="box-sizing: inherit; display: list-item; line-height: 2.4rem; margin: 0px 0px 1.2rem; padding: 0px; position: relative;"><div class="docsum-content" style="box-sizing: inherit; display: inline;"><span style="font-size: small;"><a class="docsum-title" data-ga-action="28967166" data-ga-category="similar_article" data-ga-label="" href="https://pubmed.ncbi.nlm.nih.gov/28967166/" style="background-color: transparent; box-sizing: inherit; color: #0071bc; display: inline-block; line-height: 2.4rem; margin: 0px; outline-offset: 0px; overflow-wrap: break-word; text-decoration: none;">VariantValidator: Accurate validation, mapping, and formatting of sequence variation descriptions.</a></span><div class="docsum-citation full-citation" style="box-sizing: inherit; color: #4d8055; line-height: 2.4rem;"><span style="font-size: small;"><span class="docsum-authors full-authors" style="box-sizing: inherit; color: #212121; display: block;">Freeman PJ, Hart RK, Gretton LJ, Brookes AJ, Dalgleish R.</span><span class="docsum-journal-citation full-journal-citation" style="box-sizing: inherit; display: block;">Hum Mutat. 2018 Jan;39(1):61-68. doi: 10.1002/humu.23348. Epub 2017 Oct 17.</span><span class="citation-part" style="box-sizing: inherit; display: inline-block;">PMID:<span> </span><span class="docsum-pmid" style="box-sizing: inherit;">28967166</span></span><span> </span><span class="free-resources spaced-citation-item citation-part" style="box-sizing: inherit; color: #c05600; display: inline-block; font-weight: 600; padding-left: 2.4rem;">Free PMC article.</span></span></div></div></li><li class="full-docsum" style="box-sizing: inherit; display: list-item; line-height: 2.4rem; margin: 0px 0px 1.2rem; padding: 0px; position: relative;"><div class="docsum-content" style="box-sizing: inherit; display: inline;"><span style="font-size: small;"><a class="docsum-title" data-ga-action="29936258" data-ga-category="similar_article" data-ga-label="" href="https://pubmed.ncbi.nlm.nih.gov/29936258/" style="background-color: transparent; box-sizing: inherit; color: #0071bc; display: inline-block; line-height: 2.4rem; margin: 0px; outline-offset: 0px; overflow-wrap: break-word; text-decoration: none;">Clinical Implementation and Validation of Automated Human Genome Variation Society (HGVS) Nomenclature System for Next-Generation Sequencing-Based Assays for Cancer.</a></span><div class="docsum-citation full-citation" style="box-sizing: inherit; color: #4d8055; line-height: 2.4rem;"><span style="font-size: small;"><span class="docsum-authors full-authors" style="box-sizing: inherit; color: #212121; display: block;">Callenberg KM, Santana-Santos L, Chen L, Ernst WL, De Moura MB, Nikiforov YE, Nikiforova MN, Roy S.</span><span class="docsum-journal-citation full-journal-citation" style="box-sizing: inherit; display: block;">J Mol Diagn. 2018 Sep;20(5):628-634. doi: 10.1016/j.jmoldx.2018.05.006. Epub 2018 Jun 21.</span><span class="citation-part" style="box-sizing: inherit; display: inline-block;">PMID:<span> </span><span class="docsum-pmid" style="box-sizing: inherit;">29936258</span></span></span></div></div></li></ul>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-8959227089815463704.post-18631321277876364092021-07-15T22:37:00.002+08:002021-09-17T02:24:07.034+08:00Running Kraken2 and creating a Krona report<p> Had to work with Ion Torrent BAMs for this but I think it's applicable to everything</p><p> Needed to run this on unmapped reads so running <a href="https://gist.github.com/kevin3/471c96400ceffbe3c63d728cbaaf131b">this </a>first.<br />
<script src="https://gist.github.com/kevin3/471c96400ceffbe3c63d728cbaaf131b.js"></script></p><p>After that the <a href="https://gist.github.com/kevin3/d9ec3169f3a8e1c4fe25d682483a3fca">next script </a>is fairly simple </p><p><script src="https://gist.github.com/kevin3/d9ec3169f3a8e1c4fe25d682483a3fca.js"></script>Will share the install when I have time. A major hiccup for me was realising not all pre-built db works with Kraken2</p>
Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-8959227089815463704.post-21953162166289926662021-05-13T00:53:00.002+08:002021-05-13T00:53:15.660+08:00This command allows you to see what apps are consuming internet. ss -p<p> </p><p style="line-height: 150%; margin-bottom: 10px; margin-top: 0px;">This command allows you to see what apps are consuming internet.</p>
<pre>ss -p</pre>Unknownnoreply@blogger.com1tag:blogger.com,1999:blog-8959227089815463704.post-35843227709026524112021-03-15T17:47:00.006+08:002021-03-15T17:50:56.387+08:00GenomSys Banks on MPEG-G Standard to Make Genome Analysis Mobile<p><a href="https://www.genomeweb.com/informatics/genomsys-banks-mpeg-g-standard-make-genome-analysis-mobile?utm_source=Sailthru&utm_medium=email&utm_campaign=GWDN%20Mon%20PM%202021-03-01&utm_term=GW%20Daily%20News%20Bulletin#.YE8p150zaMo" target="_blank"> This software company did something that I didn't expect.</a>.. putting the variant calling on the phone itself .. </p><p><span style="-webkit-text-stroke-width: 0px; background-color: white; color: #1d242a; display: inline; float: none; font-family: HelveticaNeueLT; font-size: 15px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-decoration-thickness: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;">"The variant calling is run directly on the phone, extracting the data from the file on your phone, processed on the phone, and only at the end the VCF file could be shared in the cloud for annotation and reporting by an accredited physician," Ascari said. The physician is necessary to assure that the result is of "diagnostic quality," he added.</span></p><p></p><p>I honestly expected <a href="https://www.internationalgenome.org/faq/what-are-cram-files/" target="_blank">CRAM</a><a href="http://kevin-gattaca.blogspot.com/2020/10/ioncram-reference-based-compression.html" target="_blank"> </a>& cloud based calling with encrypted exchange (made feasible with <a href="https://kevin-gattaca.blogspot.com/2014/11/what-5g-mobile-networks-portends-for.html" target="_blank">5G mobile network</a>) of bam reads with an app store like customised reports for what you want to know about your genetics. </p><p>Other than security concerns, I don't see why I would want variant calling on the phone though. <br /></p><h1 style="text-align: left;"></h1><p>Previous posts<br /></p><h3 class="post-title entry-title" itemprop="name"><a href="http://kevin-gattaca.blogspot.com/2020/10/ioncram-reference-based-compression.html">IonCRAM: a reference-based compression tool for ion torrent sequence files </a></h3><h3 class="post-title entry-title" itemprop="name"><a href="http://kevin-gattaca.blogspot.com/2020/10/future-of-genomics-10-bold-predictions.html">Future of Genomics: 10 bold predictions</a></h3><h3 class="post-title entry-title" itemprop="name"><a href="https://kevin-gattaca.blogspot.com/2014/11/what-5g-mobile-networks-portends-for.html">What 5G mobile networks portends for the future of personal genomics</a> <br /></h3><h3 class="post-title entry-title" itemprop="name"> </h3><h3 class="post-title entry-title" itemprop="name"> </h3><p> </p>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-8959227089815463704.post-71294806277454512842020-11-12T18:07:00.000+08:002020-11-12T18:07:08.160+08:00A novel BRCA2 splice variant identified in a young woman<p style="-webkit-text-stroke-width: 0px; background: rgb(255, 255, 255); border: 0px; box-sizing: inherit; color: rgba(0, 0, 0, 0.9); counter-reset: list-1 0 list-2 0 list-3 0 list-4 0 list-5 0 list-6 0 list-7 0 list-8 0 list-9 0; cursor: text; font-family: -apple-system, system-ui, BlinkMacSystemFont, "Segoe UI", Roboto, "Helvetica Neue", "Fira Sans", Ubuntu, Oxygen, "Oxygen Sans", Cantarell, "Droid Sans", "Apple Color Emoji", "Segoe UI Emoji", "Segoe UI Symbol", "Lucida Grande", Helvetica, Arial, sans-serif; font-size: 18px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; line-height: 1.5; margin: 0px; orphans: 2; padding: 0px; text-align: left; text-decoration-color: initial; text-decoration-style: initial; text-indent: 0px; text-transform: none; vertical-align: baseline; white-space: pre-wrap; widows: 2; word-spacing: 0px;"> Sharing a newly published article where a novel c.682‐2delA variant involving the AG consensus at the 3′ end of BRCA2 intron 8 was detected. The case involved a 33‐year‐old Italian breast cancer patient belonging to a HBOC family (BRCAPro score: 88%) with no other known pathogenic BRCA mutation. </p><p style="-webkit-text-stroke-width: 0px; background: rgb(255, 255, 255); border: 0px; box-sizing: inherit; color: rgba(0, 0, 0, 0.9); counter-reset: list-1 0 list-2 0 list-3 0 list-4 0 list-5 0 list-6 0 list-7 0 list-8 0 list-9 0; cursor: text; font-family: -apple-system, system-ui, BlinkMacSystemFont, "Segoe UI", Roboto, "Helvetica Neue", "Fira Sans", Ubuntu, Oxygen, "Oxygen Sans", Cantarell, "Droid Sans", "Apple Color Emoji", "Segoe UI Emoji", "Segoe UI Symbol", "Lucida Grande", Helvetica, Arial, sans-serif; font-size: 18px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; line-height: 1.5; margin: 0px; orphans: 2; padding: 0px; text-align: left; text-decoration-color: initial; text-decoration-style: initial; text-indent: 0px; text-transform: none; vertical-align: baseline; white-space: pre-wrap; widows: 2; word-spacing: 0px;"> </p><p style="-webkit-text-stroke-width: 0px; background: rgb(255, 255, 255); border: 0px; box-sizing: inherit; color: rgba(0, 0, 0, 0.9); counter-reset: list-1 0 list-2 0 list-3 0 list-4 0 list-5 0 list-6 0 list-7 0 list-8 0 list-9 0; cursor: text; font-family: -apple-system, system-ui, BlinkMacSystemFont, "Segoe UI", Roboto, "Helvetica Neue", "Fira Sans", Ubuntu, Oxygen, "Oxygen Sans", Cantarell, "Droid Sans", "Apple Color Emoji", "Segoe UI Emoji", "Segoe UI Symbol", "Lucida Grande", Helvetica, Arial, sans-serif; font-size: 18px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; line-height: 1.5; margin: 0px; orphans: 2; padding: 0px; text-align: left; text-decoration-color: initial; text-decoration-style: initial; text-indent: 0px; text-transform: none; vertical-align: baseline; white-space: pre-wrap; widows: 2; word-spacing: 0px;">A novel BRCA2 splice variant identified in a young woman - Nicolussi - - <a href="https://onlinelibrary.wiley.com/doi/full/10.1002/mgg3.1513 ">Molecular Genetics & Genomic Medicine </a><strong class="ql-hashtag" style="background: transparent; border: 0px; box-sizing: inherit; font-size: 18px; font-weight: 600; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;"></strong></p>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-8959227089815463704.post-48813382123375961652020-11-04T11:23:00.003+08:002020-11-04T11:23:17.948+08:00de novo assembly of Ion Torrent Reads<p> I am intrigued that this <a href="https://guilherme-neumann.com/2020/05/20/90/">Genome assembly guide</a> includes mention of SOLID and Ion Torrent ... although not much information is given on how to work on them for genome assembly. </p><p>That said, perhaps the SPADES plugin provided with the sequencer solves most of everyone's immediate needs ... Wondering how improve on evaluating the assemblies </p><p><br /></p><p><br /></p>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-8959227089815463704.post-15872518971150802352020-10-29T21:03:00.003+08:002020-10-29T21:03:55.751+08:00 IonCRAM: a reference-based compression tool for ion torrent sequence files <p> <span data-offset-key="8eeul-0-0" style="-webkit-text-stroke-width: 0px; background-color: white; color: #14171a; font-family: system-ui, -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Ubuntu, "Helvetica Neue", sans-serif; font-size: 19px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: left; text-decoration-color: initial; text-decoration-style: initial; text-indent: 0px; text-transform: none; white-space: pre-wrap; widows: 2; word-spacing: 0px;"><span data-text="true">IonCRAM: a reference-based compression tool for ion torrent sequence files </span></span><span style="-webkit-text-stroke-width: 0px; background-color: white; color: #1b95e0; font-family: system-ui, -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Ubuntu, "Helvetica Neue", sans-serif; font-size: 19px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: left; text-decoration-color: initial; text-decoration-style: initial; text-indent: 0px; text-transform: none; white-space: pre-wrap; widows: 2; word-spacing: 0px;"><span data-offset-key="8eeul-1-0"><span data-text="true">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7487613/</span></span></span><span data-offset-key="8eeul-2-0" style="-webkit-text-stroke-width: 0px; background-color: white; color: #14171a; font-family: system-ui, -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Ubuntu, "Helvetica Neue", sans-serif; font-size: 19px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: left; text-decoration-color: initial; text-decoration-style: initial; text-indent: 0px; text-transform: none; white-space: pre-wrap; widows: 2; word-spacing: 0px;"><span data-text="true"> </span></span></p><p><span data-offset-key="8eeul-2-0" style="-webkit-text-stroke-width: 0px; background-color: white; color: #14171a; font-family: system-ui, -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Ubuntu, "Helvetica Neue", sans-serif; font-size: 19px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: left; text-decoration-color: initial; text-decoration-style: initial; text-indent: 0px; text-transform: none; white-space: pre-wrap; widows: 2; word-spacing: 0px;"><span data-text="true"><span style="-webkit-text-stroke-width: 0px; background-color: white; color: black; display: inline !important; float: none; font-family: "Times New Roman", stixgeneral, serif; font-size: 15.9991px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: left; text-decoration-color: initial; text-decoration-style: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;"><span> </span>IonCRAM, the first reference-based compression tool to compress Ion Torrent BAM files for long term archiving. For the BAM files, IonCRAM could achieve a space saving of about 43%. This space saving is superior to what achieved with the CRAM format by about 8–9%.</span></span></span></p><p><span data-offset-key="8eeul-2-0" style="-webkit-text-stroke-width: 0px; background-color: white; color: #14171a; font-family: system-ui, -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Ubuntu, "Helvetica Neue", sans-serif; font-size: 19px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: left; text-decoration-color: initial; text-decoration-style: initial; text-indent: 0px; text-transform: none; white-space: pre-wrap; widows: 2; word-spacing: 0px;"><span data-text="true"><span style="-webkit-text-stroke-width: 0px; background-color: white; color: black; display: inline !important; float: none; font-family: "Times New Roman", stixgeneral, serif; font-size: 15.9991px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: left; text-decoration-color: initial; text-decoration-style: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;"></span></span></span></p><p id="Par48" style="-webkit-text-stroke-width: 0px; background-color: white; color: black; font-family: "Times New Roman", stixgeneral, serif; font-size: 15.9991px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; margin: 0.6923em 0px; orphans: 2; text-align: left; text-decoration-color: initial; text-decoration-style: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;">Future research for reducing the space consumption of the Ion Torrent BAM files would include the binning of the flow signal and quality values. The idea of binning was initially introduced by Illumina [<a aria-expanded="false" aria-haspopup="true" class=" bibr popnode" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7487613/#CR27" role="button" style="color: #642a8f;">27</a>] to reduce the space consumption of the quality values. This initiative was immediately followed by intensive research to optimize the binning procedure and address its effect on the downstream analysis, especially on the variant calling step [<a aria-expanded="false" aria-haspopup="true" class=" bibr popnode tag_hotlink tag_tooltip" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7487613/#CR28" id="__tag_880807248" role="button" style="color: #642a8f;">28</a>–<a aria-expanded="false" aria-haspopup="true" class=" bibr popnode tag_hotlink tag_tooltip" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7487613/#CR31" id="__tag_880807235" role="button" style="color: #642a8f;">31</a>]. We think that the binning of flow signals and quality data of Ion Torrent would also be successful, provided that the manufacturer contribute to this research. We added an option to IonCRAM for binning the flow signals, in a similar way to the binning method implemented in [<a aria-expanded="false" aria-haspopup="true" class=" bibr popnode tag_hotlink tag_tooltip" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7487613/#CR26" id="__tag_880807239" role="button" style="color: #642a8f;">26</a>], and measured its effect on compression (Supplementary File 1). We left the step for investigating the effect of this binning on the downstream analysis to further research.</p><p class="p p-last" id="Par49" style="-webkit-text-stroke-width: 0px; background-color: white; color: black; font-family: "Times New Roman", stixgeneral, serif; font-size: 15.9991px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; margin: 0.6923em 0px; orphans: 2; text-align: left; text-decoration-color: initial; text-decoration-style: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;">It is worth mentioning that IonCRAM has not been only used for the test data in the paper, it has also been used to compress and backup thousands of files for the Saudi Human Genome Program. IonCRAM is an open source and it is available for free along with the related test data at the tool website<span> </span><a data-ga-action="click_feat_suppl" href="http://ioncram.saudigenomeproject.com/" style="color: #642a8f;" target="_blank">http://ioncram.saudigenomeproject.com</a>.</p><p><span data-offset-key="8eeul-2-0" style="-webkit-text-stroke-width: 0px; background-color: white; color: #14171a; font-family: system-ui, -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Ubuntu, "Helvetica Neue", sans-serif; font-size: 19px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: left; text-decoration-color: initial; text-decoration-style: initial; text-indent: 0px; text-transform: none; white-space: pre-wrap; widows: 2; word-spacing: 0px;"><span data-text="true"><span style="-webkit-text-stroke-width: 0px; background-color: white; color: black; display: inline !important; float: none; font-family: "Times New Roman", stixgeneral, serif; font-size: 15.9991px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: left; text-decoration-color: initial; text-decoration-style: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;"> </span> </span></span></p>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-8959227089815463704.post-7423518195963509792020-10-29T18:31:00.000+08:002020-10-29T18:31:00.248+08:00Static ip on Jessie Raspbian with dhcpcd.conf
<br />
<h3 class="first">
<a href="https://www.raspberrypi.org/forums/viewtopic.php?t=140252#p929486">Static IP address templates for dhcpcd.conf</a></h3>
https://www.raspberrypi.org/forums/viewtopic.php?t=140252<br />
<br />
<pre><code>######################################################
# TEMPLATE: A static IP address only when no DHCP
#
# The profile name is arbitrary. Use "fred"
# if you want. Not much we can put as
# default servers, but set them up as
# you usually would.
######################################################
interface eth0
fallback nodhcp
profile nodhcp
static ip_address=10.0.0.1/8
static routers=10.0.0.1
static domain_name_servers=10.0.0.1
</code></pre>
<br />
<br />
Trying to do this<br />
<br />
https://www.diyhobi.com/share-raspberry-pi-wifi-internet-ethernet/<br />
<br />Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-8959227089815463704.post-50780111612763743142020-10-29T18:26:00.005+08:002020-10-29T18:35:46.757+08:00Future of Genomics: 10 bold predictions<p class="MsoNormal"> <span face=""Helvetica",sans-serif" style="background: white none repeat scroll 0% 0%; color: #333333; font-size: 13pt; line-height: 107%;">Curious about research
priorities and opportunities for human genomics for the next decade? You should
read on. </span></p>
<p class="MsoNormal"><span face=""Helvetica",sans-serif" style="background: white none repeat scroll 0% 0%; color: #333333; font-size: 13pt; line-height: 107%;">The National Human
Genome Research Institute (NHGRI) this week published its “Strategic vision for
improving human health at The Forefront of Genomics” </span><a data-saferedirecturl="https://www.google.com/url?q=https://genome.us12.list-manage.com/track/click?u%3D12d2aeb3c1601aea84c780560%26id%3D3428b01ecd%26e%3D3fb94b711e&source=gmail&ust=1604022001992000&usg=AFQjCNGsajZstwszCpv07U7uc25skqL3Ug" href="https://www.nature.com/articles/s41586-020-2817-4" style="-webkit-text-stroke-width: 0px; font-variant-caps: normal; font-variant-ligatures: normal; orphans: 2; widows: 2; word-spacing: 0px;" target="_blank"><b><span face=""Helvetica",sans-serif" style="background: white none repeat scroll 0% 0%; color: #001a56; font-size: 13pt; line-height: 107%;">in the journal </span></b><i><b><span face=""Helvetica",sans-serif" style="background: white none repeat scroll 0% 0%; color: #001a56; font-size: 13pt; line-height: 107%; text-decoration: none; text-underline: none;">Nature</span></b></i></a><span face=""Helvetica",sans-serif" style="background: white none repeat scroll 0% 0%; color: #333333; font-size: 13pt; line-height: 107%;"><span style="-webkit-text-stroke-width: 0px; float: none; font-variant-caps: normal; font-variant-ligatures: normal; orphans: 2; text-decoration-color: initial; text-decoration-style: initial; widows: 2; word-spacing: 0px;">. </span></span></p>
<p class="MsoNormal"><span face=""Helvetica",sans-serif" style="background: white none repeat scroll 0% 0%; color: #333333; font-size: 13pt; line-height: 107%;">The strategic vision
culminates with 10 bold predictions for human genomics by 2030. Crafted to be
both inspirational and aspirational, the predictions are intended to provoke
thoughtful discussions (and even debate) about what might be possible in the
coming decade.</span></p>
<p class="MsoNormal"><span face=""Helvetica",sans-serif" style="background: white none repeat scroll 0% 0%; color: #333333; font-size: 13pt; line-height: 107%;">I must say that <a href="https://kevin-gattaca.blogspot.com/2014/11/what-5g-mobile-networks-portends-for.html">I expected people to store their encrypted genome sequences on smartphones anduse 5G networks to launch on the fly analyses a few years back.</a> Not sure if we
will have that by 2030! </span></p><p class="MsoNormal"><span face=""Helvetica",sans-serif" style="color: #333333; font-size: 13pt; line-height: 107%;">it's also a good time to review <a href="https://kevin-gattaca.blogspot.com/2015/10/the-future-of-genomics-informatics-in.html">the 5 years prediction from 2015</a><br /> Read about <a href="https://www.genome.wustl.edu/items/reference-genome-improvement/">gold genomes and platinum genomes... </a><span style="background: white none repeat scroll 0% 0%;"><span style="-webkit-text-stroke-width: 0px; float: none; font-variant-caps: normal; font-variant-ligatures: normal; orphans: 2; text-decoration-color: initial; text-decoration-style: initial; widows: 2; word-spacing: 0px;"></span></span></span></p><p class="MsoNormal"><span face=""Helvetica",sans-serif" style="color: #333333; font-size: 13pt; line-height: 107%;"><span style="background: white none repeat scroll 0% 0%;"><span style="-webkit-text-stroke-width: 0px; float: none; font-variant-caps: normal; font-variant-ligatures: normal; orphans: 2; text-decoration-color: initial; text-decoration-style: initial; widows: 2; word-spacing: 0px;"> </span></span><br style="-webkit-text-stroke-width: 0px; font-variant-caps: normal; font-variant-ligatures: normal; orphans: 2; text-decoration-color: initial; text-decoration-style: initial; widows: 2; word-spacing: 0px;" />
<span style="background: white none repeat scroll 0% 0%;"><span style="-webkit-text-stroke-width: 0px; float: none; font-variant-caps: normal; font-variant-ligatures: normal; orphans: 2; text-decoration-color: initial; text-decoration-style: initial; widows: 2; word-spacing: 0px;">The 2020 NHGRI Strategic Vision is available online at </span></span></span><b><span face=""Helvetica",sans-serif" style="background: white none repeat scroll 0% 0%; color: black; font-size: 13pt; line-height: 107%; mso-color-alt: windowtext;"><a data-saferedirecturl="https://www.google.com/url?q=https://genome.us12.list-manage.com/track/click?u%3D12d2aeb3c1601aea84c780560%26id%3D66ba057b17%26e%3D3fb94b711e&source=gmail&ust=1604022001992000&usg=AFQjCNHN2AG_5pB2E84EE31PVcrhBTNkWQ" href="https://bit.ly/35Z57sv" style="-webkit-text-stroke-width: 0px; font-variant-caps: normal; font-variant-ligatures: normal; orphans: 2; widows: 2; word-spacing: 0px;" target="_blank">genome.gov/2020SV<span style="font-weight: normal;">.</span></a></span></b></p><p class="MsoNormal"><b><span face=""Helvetica",sans-serif" style="background: white none repeat scroll 0% 0%; color: black; font-size: 13pt; line-height: 107%; mso-color-alt: windowtext;"><span style="font-weight: normal;"> </span></span></b></p><p class="MsoNormal"><b><span face=""Helvetica",sans-serif" style="background: white none repeat scroll 0% 0%; color: black; font-size: 13pt; line-height: 107%; mso-color-alt: windowtext;"><span style="font-weight: normal;"> </span></span></b></p><p class="MsoNormal"><b><span face=""Helvetica",sans-serif" style="background: white none repeat scroll 0% 0%; color: black; font-size: 13pt; line-height: 107%; mso-color-alt: windowtext;"><span style="font-weight: normal;"> </span></span></b></p>
Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-8959227089815463704.post-43493638613335434532019-04-08T23:29:00.002+08:002019-04-08T23:29:24.951+08:00FAAH-OUT This woman feels no pain! <i>"A woman in Scotland can feel virtually no pain due to a mutation ...<br />At age 65, the woman sought treatment for an issue with her hip, which turned out to involve severe joint degeneration despite her experiencing no pain. At age 66, she underwent surgery on her hand, which is normally very painful, and yet she reported no pain after the surgery. Her pain insensitivity was diagnosed by Dr Devjit Srivastava, Consultant in Anaesthesia and Pain Medicine at an NHS hospital in the north of Scotland and co-lead author of the paper....<br />which the researchers have described for the first time and dubbed FAAH-OUT. "</i><br /><a href="https://www.sciencedaily.com/releases/2019/03/190327203450.htm">https://www.sciencedaily.com/releases/2019/03/190327203450.htm</a><br /><br /><b>Journal Reference:</b><br /><br /> Abdella M. Habib, Andrei L. Okorokov, Matthew N. Hill, Jose T. Bras, Man-Cheung Lee, Shengnan Li, Samuel J. Gossage, Marie van Drimmelen, Maria Morena, Henry Houlden, Juan D. Ramirez, David L.H. Bennett, Devjit Srivastava, James J. Cox. Microdeletion in a pseudogene identified in a patient with high anandamide concentrations and pain insensitivity. British Journal of Anaesthesia, 2019; DOI: 10.1016/j.bja.2019.02.019<br />Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-8959227089815463704.post-9488541075192679232019-03-28T22:43:00.002+08:002019-03-28T23:40:04.437+08:001-liner bash to rename spaces in filenames or folder namesSource: <a href="https://stackoverflow.com/questions/2709458/how-to-replace-spaces-in-file-names-using-a-bash-script">https://stackoverflow.com/questions/2709458/how-to-replace-spaces-in-file-names-using-a-bash-script</a><br />
#non-recursive method<br />
<pre class="lang-sh prettyprint prettyprinted" style="-webkit-text-stroke-width: 0px; background-color: #eff0f1; border-radius: 3px; border: 0px; box-sizing: inherit; color: #393318; display: block; font-family: Consolas, Menlo, Monaco, "Lucida Console", "Liberation Mono", "DejaVu Sans Mono", "Bitstream Vera Sans Mono", "Courier New", monospace, sans-serif; font-size: 13px; font-stretch: inherit; font-style: normal; font-variant-caps: normal; font-variant-east-asian: inherit; font-variant-ligatures: normal; font-variant-numeric: inherit; font-weight: 400; letter-spacing: normal; line-height: inherit; margin: 0px 0px 1em; max-height: 600px; orphans: 2; overflow-wrap: normal; overflow: auto; padding: 12px 8px; text-align: left; text-decoration-color: initial; text-decoration-style: initial; text-indent: 0px; text-transform: none; vertical-align: baseline; widows: 2; width: auto; word-spacing: 0px;"><code style="background-color: #eff0f1; border: 0px; box-sizing: inherit; font-family: Consolas, Menlo, Monaco, "Lucida Console", "Liberation Mono", "DejaVu Sans Mono", "Bitstream Vera Sans Mono", "Courier New", monospace, sans-serif; font-size: 13px; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; line-height: inherit; margin: 0px; padding: 0px; vertical-align: baseline; white-space: inherit;"><span class="kwd" style="border: 0px; box-sizing: inherit; color: #101094; font-family: inherit; font-size: 13px; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; line-height: inherit; margin: 0px; padding: 0px; vertical-align: baseline;">for</span><span class="pln" style="border: 0px; box-sizing: inherit; color: #303336; font-family: inherit; font-size: 13px; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; line-height: inherit; margin: 0px; padding: 0px; vertical-align: baseline;"> f </span><span class="kwd" style="border: 0px; box-sizing: inherit; color: #101094; font-family: inherit; font-size: 13px; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; line-height: inherit; margin: 0px; padding: 0px; vertical-align: baseline;">in</span><span class="pln" style="border: 0px; box-sizing: inherit; color: #303336; font-family: inherit; font-size: 13px; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; line-height: inherit; margin: 0px; padding: 0px; vertical-align: baseline;"> </span><span class="pun" style="border: 0px; box-sizing: inherit; color: #303336; font-family: inherit; font-size: 13px; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; line-height: inherit; margin: 0px; padding: 0px; vertical-align: baseline;">*</span><span class="pln" style="border: 0px; box-sizing: inherit; color: #303336; font-family: inherit; font-size: 13px; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; line-height: inherit; margin: 0px; padding: 0px; vertical-align: baseline;">\ </span><span class="pun" style="border: 0px; box-sizing: inherit; color: #303336; font-family: inherit; font-size: 13px; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; line-height: inherit; margin: 0px; padding: 0px; vertical-align: baseline;">*;</span><span class="pln" style="border: 0px; box-sizing: inherit; color: #303336; font-family: inherit; font-size: 13px; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; line-height: inherit; margin: 0px; padding: 0px; vertical-align: baseline;"> </span><span class="kwd" style="border: 0px; box-sizing: inherit; color: #101094; font-family: inherit; font-size: 13px; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; line-height: inherit; margin: 0px; padding: 0px; vertical-align: baseline;">do</span><span class="pln" style="border: 0px; box-sizing: inherit; color: #303336; font-family: inherit; font-size: 13px; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; line-height: inherit; margin: 0px; padding: 0px; vertical-align: baseline;"> mv </span><span class="str" style="border: 0px; box-sizing: inherit; color: #7d2727; font-family: inherit; font-size: 13px; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; line-height: inherit; margin: 0px; padding: 0px; vertical-align: baseline;">"$f"</span><span class="pln" style="border: 0px; box-sizing: inherit; color: #303336; font-family: inherit; font-size: 13px; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; line-height: inherit; margin: 0px; padding: 0px; vertical-align: baseline;"> </span><span class="str" style="border: 0px; box-sizing: inherit; color: #7d2727; font-family: inherit; font-size: 13px; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; line-height: inherit; margin: 0px; padding: 0px; vertical-align: baseline;">"${f// /_}"</span><span class="pun" style="border: 0px; box-sizing: inherit; color: #303336; font-family: inherit; font-size: 13px; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; line-height: inherit; margin: 0px; padding: 0px; vertical-align: baseline;">;</span><span class="pln" style="border: 0px; box-sizing: inherit; color: #303336; font-family: inherit; font-size: 13px; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; line-height: inherit; margin: 0px; padding: 0px; vertical-align: baseline;"> </span><span class="kwd" style="border: 0px; box-sizing: inherit; color: #101094; font-family: inherit; font-size: 13px; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; line-height: inherit; margin: 0px; padding: 0px; vertical-align: baseline;">done</span></code></pre>
Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-8959227089815463704.post-38604463189375261962019-03-28T20:47:00.001+08:002019-03-28T20:47:04.048+08:00HDD clean up; Does it spark joy?size:gigantic<br />
in Windows Explorer to look for > 128 Mb sized filesUnknownnoreply@blogger.com0tag:blogger.com,1999:blog-8959227089815463704.post-47102709083044436492018-09-29T16:46:00.002+08:002018-09-29T16:46:39.511+08:00Koala Genome assembled on AWS<br />
<!--[if gte mso 9]><xml>
<o:OfficeDocumentSettings>
<o:AllowPNG/>
</o:OfficeDocumentSettings>
</xml><![endif]--><!--[if gte mso 9]><xml>
<w:WordDocument>
<w:View>Normal</w:View>
<w:Zoom>0</w:Zoom>
<w:TrackMoves/>
<w:TrackFormatting/>
<w:PunctuationKerning/>
<w:ValidateAgainstSchemas/>
<w:SaveIfXMLInvalid>false</w:SaveIfXMLInvalid>
<w:IgnoreMixedContent>false</w:IgnoreMixedContent>
<w:AlwaysShowPlaceholderText>false</w:AlwaysShowPlaceholderText>
<w:DoNotPromoteQF/>
<w:LidThemeOther>EN-US</w:LidThemeOther>
<w:LidThemeAsian>ZH-SG</w:LidThemeAsian>
<w:LidThemeComplexScript>X-NONE</w:LidThemeComplexScript>
<w:Compatibility>
<w:BreakWrappedTables/>
<w:SnapToGridInCell/>
<w:WrapTextWithPunct/>
<w:UseAsianBreakRules/>
<w:DontGrowAutofit/>
<w:SplitPgBreakAndParaMark/>
<w:EnableOpenTypeKerning/>
<w:DontFlipMirrorIndents/>
<w:OverrideTableStyleHps/>
</w:Compatibility>
<m:mathPr>
<m:mathFont m:val="Cambria Math"/>
<m:brkBin m:val="before"/>
<m:brkBinSub m:val="--"/>
<m:smallFrac m:val="off"/>
<m:dispDef/>
<m:lMargin m:val="0"/>
<m:rMargin m:val="0"/>
<m:defJc m:val="centerGroup"/>
<m:wrapIndent m:val="1440"/>
<m:intLim m:val="subSup"/>
<m:naryLim m:val="undOvr"/>
</m:mathPr></w:WordDocument>
</xml><![endif]--><!--[if gte mso 9]><xml>
<w:LatentStyles DefLockedState="false" DefUnhideWhenUsed="true"
DefSemiHidden="true" DefQFormat="false" DefPriority="99"
LatentStyleCount="267">
<w:LsdException Locked="false" Priority="0" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Normal"/>
<w:LsdException Locked="false" Priority="9" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="heading 1"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 2"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 3"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 4"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 5"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 6"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 7"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 8"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 9"/>
<w:LsdException Locked="false" Priority="39" Name="toc 1"/>
<w:LsdException Locked="false" Priority="39" Name="toc 2"/>
<w:LsdException Locked="false" Priority="39" Name="toc 3"/>
<w:LsdException Locked="false" Priority="39" Name="toc 4"/>
<w:LsdException Locked="false" Priority="39" Name="toc 5"/>
<w:LsdException Locked="false" Priority="39" Name="toc 6"/>
<w:LsdException Locked="false" Priority="39" Name="toc 7"/>
<w:LsdException Locked="false" Priority="39" Name="toc 8"/>
<w:LsdException Locked="false" Priority="39" Name="toc 9"/>
<w:LsdException Locked="false" Priority="35" QFormat="true" Name="caption"/>
<w:LsdException Locked="false" Priority="10" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Title"/>
<w:LsdException Locked="false" Priority="1" Name="Default Paragraph Font"/>
<w:LsdException Locked="false" Priority="11" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Subtitle"/>
<w:LsdException Locked="false" Priority="22" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Strong"/>
<w:LsdException Locked="false" Priority="20" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Emphasis"/>
<w:LsdException Locked="false" Priority="59" SemiHidden="false"
UnhideWhenUsed="false" Name="Table Grid"/>
<w:LsdException Locked="false" UnhideWhenUsed="false" Name="Placeholder Text"/>
<w:LsdException Locked="false" Priority="1" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="No Spacing"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 1"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 1"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 1"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 1"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 1"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 1"/>
<w:LsdException Locked="false" UnhideWhenUsed="false" Name="Revision"/>
<w:LsdException Locked="false" Priority="34" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="List Paragraph"/>
<w:LsdException Locked="false" Priority="29" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Quote"/>
<w:LsdException Locked="false" Priority="30" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Intense Quote"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 1"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 1"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 1"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 1"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 1"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 1"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 1"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 1"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 2"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 2"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 2"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 2"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 2"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 2"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 2"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 2"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 2"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 2"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 2"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 2"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 2"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 2"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 3"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 3"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 3"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 3"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 3"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 3"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 3"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 3"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 3"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 3"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 3"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 3"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 3"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 3"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 4"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 4"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 4"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 4"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 4"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 4"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 4"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 4"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 4"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 4"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 4"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 4"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 4"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 4"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 5"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 5"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 5"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 5"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 5"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 5"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 5"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 5"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 5"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 5"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 5"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 5"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 5"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 5"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 6"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 6"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 6"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 6"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 6"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 6"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 6"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 6"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 6"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 6"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 6"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 6"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 6"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 6"/>
<w:LsdException Locked="false" Priority="19" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Subtle Emphasis"/>
<w:LsdException Locked="false" Priority="21" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Intense Emphasis"/>
<w:LsdException Locked="false" Priority="31" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Subtle Reference"/>
<w:LsdException Locked="false" Priority="32" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Intense Reference"/>
<w:LsdException Locked="false" Priority="33" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Book Title"/>
<w:LsdException Locked="false" Priority="37" Name="Bibliography"/>
<w:LsdException Locked="false" Priority="39" QFormat="true" Name="TOC Heading"/>
</w:LatentStyles>
</xml><![endif]--><!--[if gte mso 10]>
<style>
/* Style Definitions */
table.MsoNormalTable
{mso-style-name:"Table Normal";
mso-tstyle-rowband-size:0;
mso-tstyle-colband-size:0;
mso-style-noshow:yes;
mso-style-priority:99;
mso-style-parent:"";
mso-padding-alt:0in 5.4pt 0in 5.4pt;
mso-para-margin:0in;
mso-para-margin-bottom:.0001pt;
mso-pagination:widow-orphan;
font-size:10.0pt;
font-family:"Times New Roman","serif";}
</style>
<![endif]-->
<br />
<span style="font-family: "Calibri","sans-serif";">Excerpted from AWS blog </span><br />
<span style="font-family: "Calibri","sans-serif";"> </span><br />
<span style="font-family: "Calibri","sans-serif";">Five years ago, a research
team led by <a href="https://australianmuseum.net.au/staff/rebecca-johnson">Dr.
Rebecca Johnson</a> (Director of the <a href="https://australianmuseum.net.au/amri">Australian Museum Research
Institute</a>) set out to learn more about koala populations, genetics, and
diseases. As a biologically unique animal with a limited appetite, maintaining
a healthy and genetically diverse population are both key elements of any
conservation plan. In addition to characterizing the genetic diversity of koala
populations, the team wanted to strengthen Australia’s ability to lead
large-scale genome sequencing projects.</span><br />
<strong><span style="font-family: "Calibri","sans-serif"; font-size: 12.0pt; mso-ansi-language: EN-US; mso-bidi-language: AR-SA; mso-fareast-font-family: SimSun; mso-fareast-language: ZH-CN; mso-fareast-theme-font: minor-fareast;">Inside the Koala
Genome</span></strong><span style="font-family: "Calibri","sans-serif"; font-size: 12.0pt; mso-ansi-language: EN-US; mso-bidi-font-family: "Times New Roman"; mso-bidi-language: AR-SA; mso-fareast-font-family: SimSun; mso-fareast-language: ZH-CN; mso-fareast-theme-font: minor-fareast;"><br />
Last month the team published their results in <a href="https://www.nature.com/ng/">Nature Genetics</a>. Their paper (<a href="https://www.nature.com/articles/s41588-018-0153-5">Adaptation and
Conservation Insights from the Koala Genome</a>) identifies the genomic basis
for the koala’s unique biology. </span><br />
<br />
<!--[if gte mso 9]><xml>
<o:OfficeDocumentSettings>
<o:AllowPNG/>
</o:OfficeDocumentSettings>
</xml><![endif]--><!--[if gte mso 9]><xml>
<w:WordDocument>
<w:View>Normal</w:View>
<w:Zoom>0</w:Zoom>
<w:TrackMoves/>
<w:TrackFormatting/>
<w:PunctuationKerning/>
<w:ValidateAgainstSchemas/>
<w:SaveIfXMLInvalid>false</w:SaveIfXMLInvalid>
<w:IgnoreMixedContent>false</w:IgnoreMixedContent>
<w:AlwaysShowPlaceholderText>false</w:AlwaysShowPlaceholderText>
<w:DoNotPromoteQF/>
<w:LidThemeOther>EN-US</w:LidThemeOther>
<w:LidThemeAsian>ZH-SG</w:LidThemeAsian>
<w:LidThemeComplexScript>X-NONE</w:LidThemeComplexScript>
<w:Compatibility>
<w:BreakWrappedTables/>
<w:SnapToGridInCell/>
<w:WrapTextWithPunct/>
<w:UseAsianBreakRules/>
<w:DontGrowAutofit/>
<w:SplitPgBreakAndParaMark/>
<w:EnableOpenTypeKerning/>
<w:DontFlipMirrorIndents/>
<w:OverrideTableStyleHps/>
</w:Compatibility>
<m:mathPr>
<m:mathFont m:val="Cambria Math"/>
<m:brkBin m:val="before"/>
<m:brkBinSub m:val="--"/>
<m:smallFrac m:val="off"/>
<m:dispDef/>
<m:lMargin m:val="0"/>
<m:rMargin m:val="0"/>
<m:defJc m:val="centerGroup"/>
<m:wrapIndent m:val="1440"/>
<m:intLim m:val="subSup"/>
<m:naryLim m:val="undOvr"/>
</m:mathPr></w:WordDocument>
</xml><![endif]--><!--[if gte mso 9]><xml>
<w:LatentStyles DefLockedState="false" DefUnhideWhenUsed="true"
DefSemiHidden="true" DefQFormat="false" DefPriority="99"
LatentStyleCount="267">
<w:LsdException Locked="false" Priority="0" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Normal"/>
<w:LsdException Locked="false" Priority="9" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="heading 1"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 2"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 3"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 4"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 5"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 6"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 7"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 8"/>
<w:LsdException Locked="false" Priority="9" QFormat="true" Name="heading 9"/>
<w:LsdException Locked="false" Priority="39" Name="toc 1"/>
<w:LsdException Locked="false" Priority="39" Name="toc 2"/>
<w:LsdException Locked="false" Priority="39" Name="toc 3"/>
<w:LsdException Locked="false" Priority="39" Name="toc 4"/>
<w:LsdException Locked="false" Priority="39" Name="toc 5"/>
<w:LsdException Locked="false" Priority="39" Name="toc 6"/>
<w:LsdException Locked="false" Priority="39" Name="toc 7"/>
<w:LsdException Locked="false" Priority="39" Name="toc 8"/>
<w:LsdException Locked="false" Priority="39" Name="toc 9"/>
<w:LsdException Locked="false" Priority="35" QFormat="true" Name="caption"/>
<w:LsdException Locked="false" Priority="10" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Title"/>
<w:LsdException Locked="false" Priority="1" Name="Default Paragraph Font"/>
<w:LsdException Locked="false" Priority="11" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Subtitle"/>
<w:LsdException Locked="false" Priority="22" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Strong"/>
<w:LsdException Locked="false" Priority="20" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Emphasis"/>
<w:LsdException Locked="false" Priority="59" SemiHidden="false"
UnhideWhenUsed="false" Name="Table Grid"/>
<w:LsdException Locked="false" UnhideWhenUsed="false" Name="Placeholder Text"/>
<w:LsdException Locked="false" Priority="1" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="No Spacing"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 1"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 1"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 1"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 1"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 1"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 1"/>
<w:LsdException Locked="false" UnhideWhenUsed="false" Name="Revision"/>
<w:LsdException Locked="false" Priority="34" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="List Paragraph"/>
<w:LsdException Locked="false" Priority="29" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Quote"/>
<w:LsdException Locked="false" Priority="30" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Intense Quote"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 1"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 1"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 1"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 1"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 1"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 1"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 1"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 1"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 2"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 2"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 2"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 2"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 2"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 2"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 2"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 2"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 2"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 2"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 2"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 2"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 2"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 2"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 3"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 3"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 3"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 3"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 3"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 3"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 3"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 3"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 3"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 3"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 3"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 3"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 3"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 3"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 4"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 4"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 4"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 4"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 4"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 4"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 4"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 4"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 4"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 4"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 4"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 4"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 4"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 4"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 5"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 5"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 5"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 5"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 5"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 5"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 5"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 5"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 5"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 5"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 5"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 5"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 5"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 5"/>
<w:LsdException Locked="false" Priority="60" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Shading Accent 6"/>
<w:LsdException Locked="false" Priority="61" SemiHidden="false"
UnhideWhenUsed="false" Name="Light List Accent 6"/>
<w:LsdException Locked="false" Priority="62" SemiHidden="false"
UnhideWhenUsed="false" Name="Light Grid Accent 6"/>
<w:LsdException Locked="false" Priority="63" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 1 Accent 6"/>
<w:LsdException Locked="false" Priority="64" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Shading 2 Accent 6"/>
<w:LsdException Locked="false" Priority="65" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 1 Accent 6"/>
<w:LsdException Locked="false" Priority="66" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium List 2 Accent 6"/>
<w:LsdException Locked="false" Priority="67" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 1 Accent 6"/>
<w:LsdException Locked="false" Priority="68" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 2 Accent 6"/>
<w:LsdException Locked="false" Priority="69" SemiHidden="false"
UnhideWhenUsed="false" Name="Medium Grid 3 Accent 6"/>
<w:LsdException Locked="false" Priority="70" SemiHidden="false"
UnhideWhenUsed="false" Name="Dark List Accent 6"/>
<w:LsdException Locked="false" Priority="71" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Shading Accent 6"/>
<w:LsdException Locked="false" Priority="72" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful List Accent 6"/>
<w:LsdException Locked="false" Priority="73" SemiHidden="false"
UnhideWhenUsed="false" Name="Colorful Grid Accent 6"/>
<w:LsdException Locked="false" Priority="19" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Subtle Emphasis"/>
<w:LsdException Locked="false" Priority="21" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Intense Emphasis"/>
<w:LsdException Locked="false" Priority="31" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Subtle Reference"/>
<w:LsdException Locked="false" Priority="32" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Intense Reference"/>
<w:LsdException Locked="false" Priority="33" SemiHidden="false"
UnhideWhenUsed="false" QFormat="true" Name="Book Title"/>
<w:LsdException Locked="false" Priority="37" Name="Bibliography"/>
<w:LsdException Locked="false" Priority="39" QFormat="true" Name="TOC Heading"/>
</w:LatentStyles>
</xml><![endif]--><!--[if gte mso 10]>
<style>
/* Style Definitions */
table.MsoNormalTable
{mso-style-name:"Table Normal";
mso-tstyle-rowband-size:0;
mso-tstyle-colband-size:0;
mso-style-noshow:yes;
mso-style-priority:99;
mso-style-parent:"";
mso-padding-alt:0in 5.4pt 0in 5.4pt;
mso-para-margin:0in;
mso-para-margin-bottom:.0001pt;
mso-pagination:widow-orphan;
font-size:10.0pt;
font-family:"Times New Roman","serif";}
</style>
<![endif]--><span style="font-family: "Calibri","sans-serif"; font-size: 12.0pt; mso-ansi-language: EN-US; mso-bidi-font-family: "Times New Roman"; mso-bidi-language: AR-SA; mso-fareast-font-family: SimSun; mso-fareast-language: ZH-CN; mso-fareast-theme-font: minor-fareast;">This work was performed on AWS. The
research team used <a href="https://cfncluster.readthedocs.io/en/latest/">cfnCluster</a>
to create multiple clusters, each with 500 to 1000 vCPUs, and running <a href="https://github.com/PacificBiosciences/pb-assembly">Falcon</a> from <a href="https://www.pacb.com/">Pacific Biosciences</a>. All in all, the team used
3 million EC2 core hours, most of which were <a href="https://aws.amazon.com/ec2/spot/">EC2 Spot Instances</a>. </span>Unknownnoreply@blogger.com1tag:blogger.com,1999:blog-8959227089815463704.post-13722255537542879442018-09-11T20:06:00.003+08:002018-09-11T20:06:44.308+08:00BioBloom tools: fast, accurate and memory-efficient host species sequence screening using bloom filtershttps://academic.oup.com/bioinformatics/article/30/23/3402/207237<br />
<br />
<br />
<div class="wi-authors" style="-webkit-text-stroke-width: 0px; background-color: white; border: 0px; box-sizing: border-box; color: #2a2a2a; font-family: "Source Sans Pro", sans-serif; font-size: 17px; font-stretch: inherit; font-style: normal; font-variant-caps: normal; font-variant-east-asian: inherit; font-variant-ligatures: normal; font-variant-numeric: inherit; font-weight: 400; letter-spacing: normal; line-height: inherit; margin: 0px; orphans: 2; padding: 0px; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-indent: 0px; text-transform: none; vertical-align: baseline; white-space: normal; widows: 2; word-spacing: 0px;">
<div class="al-authors-list" style="border: 0px; box-sizing: border-box; font: inherit; margin: 0px 0px 11px; padding: 0px; vertical-align: baseline;">
<span class="al-author-name-more" style="border: 0px; box-sizing: border-box; display: inline-block; font: inherit; margin: 0px; padding: 0px; vertical-align: baseline;"><a class="linked-name" href="https://www.blogger.com/null" style="border: 0px; box-sizing: border-box; color: #006fb7; cursor: pointer; font: inherit; margin: 0px; overflow-wrap: break-word; padding: 0px; text-decoration: underline; vertical-align: baseline; word-break: break-word; word-wrap: break-word;">Justin Chu</a></span><span> </span><span class="al-author-name-more" style="border: 0px; box-sizing: border-box; display: inline-block; font: inherit; margin: 0px; padding: 0px; vertical-align: baseline;"><a class="linked-name" href="https://www.blogger.com/null" style="border: 0px; box-sizing: border-box; color: #006fb7; font: inherit; margin: 0px; overflow-wrap: break-word; padding: 0px; text-decoration: none; vertical-align: baseline; word-break: break-word; word-wrap: break-word;">Sara Sadeghi</a></span><span> </span><span class="al-author-name-more" style="border: 0px; box-sizing: border-box; display: inline-block; font: inherit; margin: 0px; padding: 0px; vertical-align: baseline;"><a class="linked-name" href="https://www.blogger.com/null" style="border: 0px; box-sizing: border-box; color: #006fb7; font: inherit; margin: 0px; overflow-wrap: break-word; padding: 0px; text-decoration: none; vertical-align: baseline; word-break: break-word; word-wrap: break-word;">Anthony Raymond</a></span><span> </span><span class="al-author-name-more" style="border: 0px; box-sizing: border-box; display: inline-block; font: inherit; margin: 0px; padding: 0px; vertical-align: baseline;"><a class="linked-name" href="https://www.blogger.com/null" style="border: 0px; box-sizing: border-box; color: #006fb7; font: inherit; margin: 0px; overflow-wrap: break-word; padding: 0px; text-decoration: none; vertical-align: baseline; word-break: break-word; word-wrap: break-word;">Shaun D. Jackman</a></span><span> </span><span class="al-author-name-more" style="border: 0px; box-sizing: border-box; display: inline-block; font: inherit; margin: 0px; padding: 0px; vertical-align: baseline;"><a class="linked-name" href="https://www.blogger.com/null" style="border: 0px; box-sizing: border-box; color: #006fb7; font: inherit; margin: 0px; overflow-wrap: break-word; padding: 0px; text-decoration: none; vertical-align: baseline; word-break: break-word; word-wrap: break-word;">Ka Ming Nip</a></span><span class="al-author-name-more" style="border: 0px; box-sizing: border-box; display: inline-block; font: inherit; margin: 0px; padding: 0px; vertical-align: baseline;"><a class="linked-name" href="https://www.blogger.com/null" style="border: 0px; box-sizing: border-box; color: #006fb7; font: inherit; margin: 0px; overflow-wrap: break-word; padding: 0px; text-decoration: none; vertical-align: baseline; word-break: break-word; word-wrap: break-word;">Richard Mar</a></span><span> </span><span class="al-author-name-more" style="border: 0px; box-sizing: border-box; display: inline-block; font: inherit; margin: 0px; padding: 0px; vertical-align: baseline;"><a class="linked-name" href="https://www.blogger.com/null" style="border: 0px; box-sizing: border-box; color: #006fb7; font: inherit; margin: 0px; overflow-wrap: break-word; padding: 0px; text-decoration: none; vertical-align: baseline; word-break: break-word; word-wrap: break-word;">Hamid Mohamadi</a></span><span> </span><span class="al-author-name-more" style="border: 0px; box-sizing: border-box; display: inline-block; font: inherit; margin: 0px; padding: 0px; vertical-align: baseline;"><a class="linked-name" href="https://www.blogger.com/null" style="border: 0px; box-sizing: border-box; color: #006fb7; font: inherit; margin: 0px; overflow-wrap: break-word; padding: 0px; text-decoration: none; vertical-align: baseline; word-break: break-word; word-wrap: break-word;">Yaron S. Butterfield</a></span><span> </span><span class="al-author-name-more" style="border: 0px; box-sizing: border-box; display: inline-block; font: inherit; margin: 0px; padding: 0px; vertical-align: baseline;"><a class="linked-name" href="https://www.blogger.com/null" style="border: 0px; box-sizing: border-box; color: #006fb7; font: inherit; margin: 0px; overflow-wrap: break-word; padding: 0px; text-decoration: none; vertical-align: baseline; word-break: break-word; word-wrap: break-word;">A. Gordon Robertson</a></span><span> </span><span class="al-author-name-more" style="border: 0px; box-sizing: border-box; display: inline-block; font: inherit; margin: 0px; padding: 0px; vertical-align: baseline;"><a class="linked-name" href="https://www.blogger.com/null" style="border: 0px; box-sizing: border-box; color: #006fb7; font: inherit; margin: 0px; overflow-wrap: break-word; padding: 0px; text-decoration: none; vertical-align: baseline; word-break: break-word; word-wrap: break-word;">Inanç Birol</a></span></div>
</div>
<div class="pub-history-wrap clearfix" style="-webkit-text-stroke-width: 0px; background-color: white; border: 0px; box-sizing: border-box; color: #2a2a2a; font-family: "Source Sans Pro", sans-serif; font-size: 17px; font-stretch: inherit; font-style: normal; font-variant-caps: normal; font-variant-east-asian: inherit; font-variant-ligatures: normal; font-variant-numeric: inherit; font-weight: 400; letter-spacing: normal; line-height: inherit; margin: 11px 0px; orphans: 2; padding: 0px; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-indent: 0px; text-transform: none; vertical-align: baseline; white-space: normal; widows: 2; word-spacing: 0px;">
<div class="pub-history-row clearfix" style="border: 0px; box-sizing: border-box; font: inherit; margin: 0px; padding: 0px; vertical-align: baseline;">
<div class="ww-citation-primary" style="border: 0px; box-sizing: border-box; display: inline; font: inherit; margin: 0px 15px 0px 0px; padding: 0px; vertical-align: baseline;">
<em style="border: 0px; box-sizing: border-box; font-family: inherit; font-size: inherit; font-stretch: inherit; font-style: italic; font-variant: inherit; font-weight: inherit; line-height: inherit; margin: 0px; padding: 0px; vertical-align: baseline;">Bioinformatics</em>, Volume 30, Issue 23, 1 December 2014, Pages 3402–3404,<a href="https://doi.org/10.1093/bioinformatics/btu558" style="border: 0px; box-sizing: border-box; color: #006fb7; font: inherit; margin: 0px; overflow-wrap: break-word; padding: 0px; text-decoration: none; vertical-align: baseline; word-break: break-word; word-wrap: break-word;">https://doi.org/10.1093/bioinformatics/btu558</a></div>
</div>
<div class="pub-history-row clearfix" style="border: 0px; box-sizing: border-box; font: inherit; margin: 0px; padding: 0px; vertical-align: baseline;">
<div class="ww-citation-date-wrap" style="border: 0px; box-sizing: border-box; display: inline-block; font: inherit; margin: 0px 20px 0px 0px; padding: 0px; vertical-align: baseline;">
<div class="citation-label" style="border: 0px; box-sizing: border-box; display: inline; font-family: inherit; font-size: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-weight: bold; line-height: inherit; margin: 0px 5px 0px 0px; padding: 0px; vertical-align: baseline;">
Published:</div>
<span> </span><div class="citation-date" style="border: 0px; box-sizing: border-box; display: inline; font: inherit; margin: 0px; padding: 0px; vertical-align: baseline;">
20 August 2014</div>
</div>
</div>
<div class="pub-history-row clearfix" style="border: 0px; box-sizing: border-box; font: inherit; margin: 0px; padding: 0px; vertical-align: baseline;">
<div class="ww-citation-date-wrap" style="border: 0px; box-sizing: border-box; display: inline-block; font: inherit; margin: 0px 20px 0px 0px; padding: 0px; vertical-align: baseline;">
<div class="citation-date" style="border: 0px; box-sizing: border-box; display: inline; font: inherit; margin: 0px; padding: 0px; vertical-align: baseline;">
</div>
</div>
</div>
<div class="pub-history-row clearfix" style="border: 0px; box-sizing: border-box; font: inherit; margin: 0px; padding: 0px; vertical-align: baseline;">
<div class="ww-citation-date-wrap" style="border: 0px; box-sizing: border-box; display: inline-block; font: inherit; margin: 0px 20px 0px 0px; padding: 0px; vertical-align: baseline;">
<div class="citation-date" style="border: 0px; box-sizing: border-box; display: inline; font: inherit; margin: 0px; padding: 0px; vertical-align: baseline;">
<h2 class="abstract-title" id="84889505" style="-webkit-text-stroke-width: 0px; background: rgb(239, 242, 247); border: 0px; box-sizing: border-box; color: #2a2a2a; font-family: "Source Sans Pro", sans-serif; font-size: 1.25rem !important; font-stretch: inherit; font-style: normal; font-variant-caps: normal; font-variant-east-asian: inherit; font-variant-ligatures: normal; font-variant-numeric: inherit; font-weight: bold; letter-spacing: normal; line-height: 1em; margin-bottom: 0px !important; margin-left: 0px; margin-right: 0px; margin-top: 0px; orphans: 2; padding: 1.5rem 1.2rem 0.9rem; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-indent: 0px; text-transform: none; vertical-align: baseline; white-space: normal; widows: 2; word-spacing: 0px;">
Abstract</h2>
<section class="abstract" style="-webkit-text-stroke-width: 0px; background: rgb(239, 242, 247); border: 0px; box-sizing: border-box; color: #2a2a2a; display: block; font-family: Merriweather, serif; font-size: medium; font-stretch: inherit; font-style: normal; font-variant-caps: normal; font-variant-east-asian: inherit; font-variant-ligatures: normal; font-variant-numeric: inherit; font-weight: 400; letter-spacing: normal; line-height: inherit; margin: 0px; orphans: 2; padding: 0px 1.2rem 1.7rem; position: relative; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-indent: 0px; text-transform: none; vertical-align: baseline; white-space: normal; widows: 2; word-spacing: 0px;"><div style="border: 0px; box-sizing: border-box; font-family: inherit; font-size: 15px; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; line-height: 1.7em; margin: 0px 0px 0.6rem; padding: 0px; vertical-align: baseline;">
Large datasets can be screened for sequences from a specific organism, quickly and with low memory requirements, by a data structure that supports time- and memory-efficient set membership queries. Bloom filters offer such queries but require that false positives be controlled. We present BioBloom Tools, a Bloom filter-based sequence-screening tool that is faster than BWA, Bowtie 2 (popular alignment algorithms) and FACS (a membership query algorithm). It delivers accuracies comparable with these tools, controls false positives and has low memory requirements.</div>
<div style="border: 0px; box-sizing: border-box; font-family: inherit; font-size: 15px; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; line-height: 1.7em; margin: 0px 0px 0.6rem; padding: 0px; vertical-align: baseline;">
<strong style="border: 0px; box-sizing: border-box; font-family: inherit; font-size: inherit; font-stretch: inherit; font-style: inherit; font-variant: inherit; font-weight: bold; line-height: inherit; margin: 0px; padding: 0px; vertical-align: baseline;">Availability and implementaion:</strong><a class="link link-uri" href="http://www.bcgsc.ca/platform/bioinfo/software/biobloomtools" style="border: 0px; box-sizing: border-box; color: #006fb7; font: inherit; margin: 0px; overflow-wrap: break-word; padding: 0px; text-decoration: none; vertical-align: baseline; word-break: break-word; word-wrap: break-word;" target="">www.bcgsc.ca/platform/bioinfo/software/biobloomtools</a></div>
</section> </div>
</div>
</div>
</div>
Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-8959227089815463704.post-53198547210681406532018-03-20T00:57:00.003+08:002018-03-20T00:57:53.498+08:00JD: Sr. Software DevOps Engineer at Guardant Health<span style="-webkit-text-stroke-width: 0px; background-color: white; color: #2e343d; display: inline !important; float: none; font-family: Arimo, Tahoma, 나눔고딕, NanumGothic, 나눔고딕, "맑은 고딕", "Malgun Gothic", "맑은 고딕", 돋움, Dotum, 돋움, sans-serif; font-size: 12px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;">https://jobs.smartrecruiters.com/GuardantHealth/743999667525776-sr-software-devops-engineer</span><br />
<span style="-webkit-text-stroke-width: 0px; background-color: white; color: #2e343d; display: inline !important; float: none; font-family: Arimo, Tahoma, 나눔고딕, NanumGothic, 나눔고딕, "맑은 고딕", "Malgun Gothic", "맑은 고딕", 돋움, Dotum, 돋움, sans-serif; font-size: 12px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;">Gotta love this line </span><br />
<i><span style="-webkit-text-stroke-width: 0px; background-color: white; color: #2e343d; display: inline !important; float: none; font-family: Arimo, Tahoma, 나눔고딕, NanumGothic, 나눔고딕, "맑은 고딕", "Malgun Gothic", "맑은 고딕", 돋움, Dotum, 돋움, sans-serif; font-size: 12px; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;"><span style="-webkit-text-stroke-width: 0px; background-color: white; color: #444545; display: inline !important; float: none; font-family: "Helvetica Neue", Arial, sans-serif; font-size: 14px; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;">“We wanted flying cars and instead we got 140 characters” is a much-repeated complaint about Silicon Valley. But with all due respect to flying cars, we believe that our mission is even more critical.<span> </span></span></span></i><br />
<br />
<span style="-webkit-text-stroke-width: 0px; background-color: white; color: #2e343d; display: inline !important; float: none; font-family: Arimo, Tahoma, 나눔고딕, NanumGothic, 나눔고딕, "맑은 고딕", "Malgun Gothic", "맑은 고딕", 돋움, Dotum, 돋움, sans-serif; font-size: 12px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;"><span style="-webkit-text-stroke-width: 0px; background-color: white; color: #444545; display: inline !important; float: none; font-family: "Helvetica Neue", Arial, sans-serif; font-size: 14px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;"><span><u><b>notable skills in the JD to pursue</b></u> </span></span></span><br />
<span style="-webkit-text-stroke-width: 0px; background-color: white; color: #2e343d; display: inline !important; float: none; font-family: Arimo, Tahoma, 나눔고딕, NanumGothic, 나눔고딕, "맑은 고딕", "Malgun Gothic", "맑은 고딕", 돋움, Dotum, 돋움, sans-serif; font-size: 12px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;"><span style="-webkit-text-stroke-width: 0px; background-color: white; color: #444545; display: inline !important; float: none; font-family: "Helvetica Neue", Arial, sans-serif; font-size: 14px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;"><span>Ansible / Chef</span></span></span><br />
<span style="-webkit-text-stroke-width: 0px; background-color: white; color: #2e343d; display: inline !important; float: none; font-family: Arimo, Tahoma, 나눔고딕, NanumGothic, 나눔고딕, "맑은 고딕", "Malgun Gothic", "맑은 고딕", 돋움, Dotum, 돋움, sans-serif; font-size: 12px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;"><span style="-webkit-text-stroke-width: 0px; background-color: white; color: #444545; display: inline !important; float: none; font-family: "Helvetica Neue", Arial, sans-serif; font-size: 14px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;"><span>Docker</span></span></span><br />
<br />
<br />
<span style="-webkit-text-stroke-width: 0px; background-color: white; color: #2e343d; display: inline !important; float: none; font-family: Arimo, Tahoma, 나눔고딕, NanumGothic, 나눔고딕, "맑은 고딕", "Malgun Gothic", "맑은 고딕", 돋움, Dotum, 돋움, sans-serif; font-size: 12px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;"><span style="-webkit-text-stroke-width: 0px; background-color: white; color: #444545; display: inline !important; float: none; font-family: "Helvetica Neue", Arial, sans-serif; font-size: 14px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;"><span>This paragraph sounds exactly like what I face on a daily basis</span></span></span><br />
<br />
<span style="-webkit-text-stroke-width: 0px; background-color: white; color: #2e343d; display: inline !important; float: none; font-family: Arimo, Tahoma, 나눔고딕, NanumGothic, 나눔고딕, "맑은 고딕", "Malgun Gothic", "맑은 고딕", 돋움, Dotum, 돋움, sans-serif; font-size: 12px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;"><span style="-webkit-text-stroke-width: 0px; background-color: white; color: #444545; display: inline !important; float: none; font-family: "Helvetica Neue", Arial, sans-serif; font-size: 14px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;"><span><i><span style="-webkit-text-stroke-width: 0px; background-color: white; color: #444545; display: inline !important; float: none; font-family: "Helvetica Neue", Arial, sans-serif; font-size: 14px; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;">Your troubleshooting skills are excellent, and you enjoy a good daily challenge in supporting rapid growth and a diverse set of end user needs. You have the ability to maintain day to day support while running various key projects that move the business forward by automating and creating new tools that facilitate management of the environment.</span></i> </span></span></span><br />
<span style="-webkit-text-stroke-width: 0px; background-color: white; color: #2e343d; display: inline !important; float: none; font-family: Arimo, Tahoma, 나눔고딕, NanumGothic, 나눔고딕, "맑은 고딕", "Malgun Gothic", "맑은 고딕", 돋움, Dotum, 돋움, sans-serif; font-size: 12px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;"><span style="-webkit-text-stroke-width: 0px; background-color: white; color: #444545; display: inline !important; float: none; font-family: "Helvetica Neue", Arial, sans-serif; font-size: 14px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;"><span> </span></span> </span>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-8959227089815463704.post-42514633799203363962018-02-23T00:14:00.001+08:002018-02-23T00:14:20.348+08:00Exploring the 1000 genome dataset with Hail on Amazon EMR and Amazon Athena Blog post from Roy Hasson <br />
<br />
https://aws.amazon.com/blogs/big-data/genomic-analysis-with-hail-on-amazon-emr-and-amazon-athena/?nc1=b_rp<br />
<i><br /></i>
<div style="-webkit-text-stroke-width: 0px; box-sizing: border-box; color: #333333; font-family: AmazonEmber, "Helvetica Neue", Helvetica, Arial, sans-serif; font-size: 14px; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;">
<i>Genomics analysis has taken off in recent years as organizations continue to adopt the cloud for its elasticity, durability, and cost. With the AWS Cloud, customers have a number of performant options to choose from. These options include<span> </span><a href="https://aws.amazon.com/batch/" rel="noopener noreferrer" style="background-color: transparent; box-sizing: border-box; color: #005b86; outline: 0px; text-decoration: none;" target="_blank">AWS Batch</a><span> </span>in conjunction with<span> </span><a href="https://aws.amazon.com/lambda" rel="noopener noreferrer" style="background-color: transparent; box-sizing: border-box; color: #005b86; outline: 0px; text-decoration: none;" target="_blank">AWS Lambda</a><span> </span>and<span> </span><a href="https://aws.amazon.com/step-functions" rel="noopener noreferrer" style="background-color: transparent; box-sizing: border-box; color: #005b86; outline: 0px; text-decoration: none;" target="_blank">AWS Step Functions</a>;<span> </span><a href="https://aws.amazon.com/glue/" rel="noopener noreferrer" style="background-color: transparent; box-sizing: border-box; color: #005b86; outline: 0px; text-decoration: none;" target="_blank">AWS Glue</a>, a serverless extract, transform, and load (ETL) service; and of course, the AWS big data and machine learning workhorse<span> </span><a href="https://aws.amazon.com/emr/" rel="noopener noreferrer" style="background-color: transparent; box-sizing: border-box; color: #005b86; outline: 0px; text-decoration: none;" target="_blank">Amazon EMR</a>.</i></div>
<div style="-webkit-text-stroke-width: 0px; box-sizing: border-box; color: #333333; font-family: AmazonEmber, "Helvetica Neue", Helvetica, Arial, sans-serif; font-size: 14px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;">
<i>For this task, we use<span> </span><a href="https://hail.is/" style="background-color: transparent; box-sizing: border-box; color: #005b86; outline: 0px; text-decoration: none;">Hail</a>, an open source framework for exploring and analyzing genomic data that uses the Apache Spark framework. In this post, we use Amazon EMR to run Hail. We walk through the setup, configuration, and data processing. Finally, we generate an Apache Parquet–formatted variant dataset and explore it using<span> </span><a href="https://aws.amazon.com/athena/" style="background-color: transparent; box-sizing: border-box; color: #005b86; outline: 0px; text-decoration: none;">Amazon Athena</a>. </i></div>
Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-8959227089815463704.post-90168912381025677592017-12-08T12:02:00.001+08:002017-12-08T12:02:22.460+08:00 Job: DATA SCIENTIST--WATSON HEALTH-CAMBRIDGE, MA.<div class="post vote-box visible-lg visible-md" data-post_id="210796" style="-webkit-text-stroke-width: 0px; background-color: white; box-sizing: border-box; color: #333333; display: block; float: left; font-family: sans-serif; font-size: 13px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; margin-left: -10px; orphans: 2; text-align: center; text-decoration-color: initial; text-decoration-style: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; width: 60px; word-spacing: 0px;">
<div class="count" itemprop="voteCount" style="box-sizing: border-box; font-size: 31.2px; font-weight: bold; margin: 5px 0px; text-align: center;">
</div>
<div class="count" itemprop="voteCount" style="box-sizing: border-box; font-size: 31.2px; font-weight: bold; margin: 5px 0px; text-align: center;">
<br class="Apple-interchange-newline" /></div>
</div>
<div style="-webkit-text-stroke-width: 0px; background-color: white; box-sizing: border-box; color: #333333; font-family: sans-serif; font-size: 13px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;">
<a href="https://www.blogger.com/null" name="210796" style="background: transparent; box-sizing: border-box; color: #428bca; text-decoration: none;"></a><div class="content" style="box-sizing: border-box; min-height: 8em; overflow: auto;">
<div class="col-xs-3 col-md-2 box pull-right text-center visible-lg visible-md" style="background-color: whitesmoke; border-radius: 4px; border: 1px solid rgb(211, 211, 211); box-sizing: border-box; display: block !important; float: right; font-size: small; margin-left: 10px; min-height: 1px; padding: 10px 0px; position: relative; text-align: center; width: 132.917px;">
<div class="ago" style="box-sizing: border-box; color: grey;">
15 months ago by</div>
<div class="uname" style="box-sizing: border-box;">
<a href="https://www.biostars.org/u/28045/" style="background: transparent; box-sizing: border-box; color: #428bca; text-decoration: none;">cshevlin</a><span> </span>•<span> </span><b style="box-sizing: border-box; font-weight: bold;">40</b></div>
</div>
<span itemprop="text" style="box-sizing: border-box;"><div style="box-sizing: border-box; margin: 0px 0px 10px;">
Spotted this ad in Biostars .. https://www.biostars.org/p/210796/ </div>
<div style="box-sizing: border-box; margin: 0px 0px 10px;">
<br /></div>
<div style="box-sizing: border-box; margin: 0px 0px 10px;">
<br /></div>
<div style="box-sizing: border-box; margin: 0px 0px 10px;">
The IBM Watson Health business division is now looking for talented individuals destined to usher in the next era of healthcare. We live in a moment of remarkable change and opportunity. The convergence of data and technology is transforming healthcare and life sciences organizations in every way. New roles are being created that never existed before to meet the demands of this transformation.</div>
<div style="box-sizing: border-box; margin: 0px 0px 10px;">
Link:<span> </span><a href="http://ibm.biz/BdruNd" rel="nofollow" style="background: transparent; box-sizing: border-box; color: #428bca; text-decoration: none;">http://ibm.biz/BdruNd</a></div>
<div style="box-sizing: border-box; margin: 0px 0px 10px;">
We are now looking for a Genomic Data Scientist to join our team.</div>
<div style="box-sizing: border-box; margin: 0px 0px 10px;">
You will have an opportunity to work directly with the team building new healthcare solutions using genomic analytics and serving oncologists, pathologists and other specialists caring for patients. You will help define, design, and build those solutions and apply your expertise to work in different analytical and statistical models.</div>
<div style="box-sizing: border-box; margin: 0px 0px 10px;">
<strong style="box-sizing: border-box; font-weight: bold;">Key Responsibilities:</strong><span> </span>Develop tools to transform load and validate data Strategizes new uses for data and its interaction with data design Perform data studies of new and diverse data sources Find new uses for existing data sources Discover “stories” told by the data and presents them to other scientists and business managers Generate algorithms and create computer models<em style="box-sizing: border-box;">*</em>*</div>
<div style="box-sizing: border-box; margin: 0px 0px 10px;">
Ideal Candidates will possess the following:</div>
<div style="box-sizing: border-box; margin: 0px 0px 10px;">
<strong style="box-sizing: border-box; font-weight: bold;">Candidates should foremost have a strong background in data mining and statistics. Hands-on background in programming and using databases and tools to mine data including practical experience in extracting, transforming and load data as well as developing statistical and analytical models. Candidates must have demonstrated capacity to adapt to demanding and high pressure projects and adaptability to client’s needs. Background on bioinformatics Experience in Healthcare or Life Sciences</strong></div>
<div style="box-sizing: border-box; margin: 0px 0px 10px;">
Learn more about IBM Watson Health and what we are doing …. And apply Now to explore this opportunity with us!</div>
<div style="box-sizing: border-box; margin: 0px 0px 10px;">
*U.S. Department of Veterans Affairs Enlists IBM’s Watson in the War on Cancer Public-Private Partnership Will Help Doctors Scale Precision Medicine Access for up to 10,000 VA Cancer Patients<span> </span><a href="http://www-03.ibm.com/press/us/en/pressrelease/50061.wss" rel="nofollow" style="background: transparent; box-sizing: border-box; color: #428bca; text-decoration: none;">http://www-03.ibm.com/press/us/en/pressrelease/50061.wss</a></div>
<div style="box-sizing: border-box; margin: 0px 0px 10px;">
IBM and New York Genome Center’s new cancer tumor repository aims to revolutionize treatment</div>
<div style="box-sizing: border-box; margin: 0px 0px 10px;">
IBM's Watson to help doctors devise optimal cancer treatment</div>
<div style="box-sizing: border-box; margin: 0px 0px 10px;">
Employment Type</div>
<div style="box-sizing: border-box; margin: 0px 0px 10px;">
Full-Time</div>
<div style="box-sizing: border-box; margin: 0px 0px 10px;">
<strong style="box-sizing: border-box; font-weight: bold;">Required Technical and Professional Expertise At least 2 years of experience in data mining At least 1 year of experience with one or more data/statistics tools, such as Python, R, SPSS, Perl At least 1 year of programming Demonstrated ability in effective communication skills</strong></div>
<div style="box-sizing: border-box; margin: 0px 0px 10px;">
Fluent in English</div>
<div style="box-sizing: border-box; margin: 0px 0px 10px;">
<strong style="box-sizing: border-box; font-weight: bold;">Preferred Technical and Professional Experience 3 years of experience with one or more data/statistics tools such as Python, R, SPSS 1 year of experience with relational databases, such as DB2, NoSQL, etc</strong></div>
</span></div>
</div>
Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-8959227089815463704.post-1581887723908525992017-08-13T13:21:00.003+08:002017-08-13T13:21:47.797+08:00Meet Nephele: Harness the Power of the Cloud for Your Microbiome Data Analysis<span itemprop="text" style="-webkit-text-stroke-width: 0px; background-color: white; box-sizing: border-box; color: #333333; font-family: sans-serif; font-size: 13px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;"></span><br />
<h2 style="box-sizing: border-box; color: inherit; font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; font-size: 1.6em; font-weight: 500; line-height: 1.1; margin-bottom: 10px; margin-top: 20px;">
<span style="-webkit-text-stroke-width: 0px; background-color: white; color: #333333; display: inline !important; float: none; font-family: sans-serif; font-size: 13px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;">Nephele is a project from the National Institutes of Health (NIH) that brings together microbiome data and analysis tools in a cloud computing environment. It aims to address a major challenge facing researchers today — namely, analyzing, transferring, and storing biomedical "big data" — through the use of cloud-based resources</span></h2>
<h2 style="box-sizing: border-box; color: inherit; font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; font-size: 1.6em; font-weight: 500; line-height: 1.1; margin-bottom: 10px; margin-top: 20px;">
<span style="-webkit-text-stroke-width: 0px; background-color: white; color: #333333; display: inline !important; float: none; font-family: sans-serif; font-size: 13px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;"> </span>Why Use Nephele?</h2>
<ul style="box-sizing: border-box; margin-bottom: 10px; margin-top: 0px;">
<li style="box-sizing: border-box;">Liberating: Nephele enables you to break free from constraints imposed on high-throughput computational analysis</li>
<li style="box-sizing: border-box;">Simple: Nephele is designed to be a no-hassle, easy-to-use tool to support your research</li>
<li style="box-sizing: border-box;">Sophisticated: Nephele is the most intuitive, advanced and secure microbiome analysis platform designed by our experienced computational biologists and software development team to provide exceptional capability with little effort on your part</li>
<li style="box-sizing: border-box;">Fast: Nephele speeds up microbiome data analysis and paves the path to getting to your results</li>
<li style="box-sizing: border-box;">Economical: Nephele's on-demand, pay-as-you-go setup offers a cost-effective alternative to using of dedicated resources for your microbiome data analysis</li>
</ul>
<div style="box-sizing: border-box; margin: 0px 0px 10px;">
Ready to get started? Visit<span> </span><a href="https://nephele.niaid.nih.gov/" rel="nofollow" style="background: transparent; box-sizing: border-box; color: #428bca; text-decoration: none;">https://nephele.niaid.nih.gov/</a><span> </span>and enter your email address. Check your inbox for a message with the subject "Your Nephele Promotional Codes."</div>
<div style="box-sizing: border-box; margin: 0px 0px 10px;">
Stay in touch! Email nephele@mail.nih.gov with your questions and feedback. You can also visit our Google+ community page to connect with other researchers in the microbiome community (<a href="https://plus.google.com/communities/107278901311674483366)" rel="nofollow" style="background: transparent; box-sizing: border-box; color: #428bca; text-decoration: none;">https://plus.google.com/communities/107278901311674483366)</a>.</div>
<span style="-webkit-text-stroke-width: 0px; background-color: white; color: #333333; display: inline !important; float: none; font-family: sans-serif; font-size: 13px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;"></span><br />
<div class="clearfix" style="-webkit-text-stroke-width: 0px; background-color: white; box-sizing: border-box; color: #333333; font-family: sans-serif; font-size: 13px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;">
<div class="tags clearfix" style="box-sizing: border-box; margin-bottom: 0.5em;">
Source: https://www.biostars.org/p/204081/</div>
<div class="tags clearfix" style="box-sizing: border-box; margin-bottom: 0.5em;">
<br class="Apple-interchange-newline" /></div>
</div>
Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-8959227089815463704.post-9589832877310241392017-08-13T13:18:00.002+08:002021-09-17T02:30:05.253+08:00demo bam file Ion Torrent 314 chip of E. coli 400 bp run for download<br />
BAM file of B22-730 (314v2 E. coli 400 bp run) <br />
Ion Torrent PGM 314v2 run with a mode read length of 400bp and per-base raw read accuracy >99%.<br />
<br />
<a href="https://s3.amazonaws.com/ion-torrent/pgm/B22-730/B22-730.bam">https://s3.amazonaws.com/ion-torrent/pgm/B22-730/B22-730.bam</a><br />
<br />
Source: <a href="https://apps.thermofisher.com/apps/publiclib/#/datasets">https://apps.thermofisher.com/apps/publiclib/#/datasets</a><br />
<br />Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-8959227089815463704.post-81834269853265410932017-08-02T17:01:00.002+08:002017-08-02T17:01:20.510+08:00Creating filtered fastq files of ONLY mapped reads from a BAM file<h3 dir="ltr" style="line-height: 1.38; margin-bottom: 4pt; margin-top: 16pt;">
<span style="background-color: transparent; color: #434343; font-family: Arial; font-size: 14pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Filtering BAM files for mapped or unmapped reads</span></h3>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">To get the </span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">unmapped</span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> reads from a</span><a href="http://samtools.sourceforge.net/SAM1.pdf" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> </span><span style="background-color: transparent; color: #1155cc; font-family: Arial; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">bam</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> file use :</span></div>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">samtools view -f 4 file.bam > unmapped.sam, the output will be in</span><a href="http://samtools.sourceforge.net/SAM1.pdf" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> </span><span style="background-color: transparent; color: #1155cc; font-family: Arial; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">sam</span></a></div>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">to get the output in</span><a href="http://samtools.sourceforge.net/SAM1.pdf" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> </span><span style="background-color: transparent; color: #1155cc; font-family: Arial; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">bam</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> use : samtools view -b -f 4 file.bam > unmapped.bam</span></div>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">To get only the </span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">mapped</span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> reads use the parameter 'F', which works like -v of grep and skips the alignments for a specific flag.</span></div>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">samtools view -b -F 4 file.bam > mapped.bam</span></div>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br /></span></div>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Source: <a href="https://www.biostars.org/p/56246/">https://www.biostars.org/p/56246/</a> Sukhdeep Singh</span></div>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 11pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br /></span></div>
<b id="docs-internal-guid-6d800070-a229-ee50-e06d-adcaa08f3ec0" style="font-weight: normal;"><br /></b>
<div dir="ltr" style="background-color: white; line-height: 1.38; margin-bottom: 8pt; margin-top: 0pt;">
<span style="background-color: transparent; color: #333333; font-family: Arial; font-size: 10pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">To do this as efficiently as possible, using </span><a href="http://sourceforge.net/projects/bbmap/" style="text-decoration: none;"><span style="background-color: transparent; color: #428bca; font-family: Arial; font-size: 10pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">BBTools</span></a><span style="background-color: transparent; color: #333333; font-family: Arial; font-size: 10pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">:</span></div>
<div dir="ltr" style="background-color: white; line-height: 1.38; margin-bottom: 8pt; margin-top: 0pt;">
<span style="background-color: transparent; color: #333333; font-family: Arial; font-size: 10pt; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">reformat.sh in=reads.sam out=mapped.fq mappedonly</span></div>
<div dir="ltr" style="background-color: white; line-height: 1.38; margin-bottom: 8pt; margin-top: 0pt;">
<span style="background-color: transparent; color: #333333; font-family: Arial; font-size: 10pt; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Also, BBMap has a lot of options designed for filtering, so it can output in fastq format and separate mapped from unmapped reads, preventing the creation of intermediate sam files. This approach also keeps pairs together, which is not very easy using samtools for filtering.</span></div>
<br />
<div dir="ltr" style="background-color: white; line-height: 1.38; margin-bottom: 8pt; margin-top: 0pt;">
<span style="background-color: transparent; color: #333333; font-family: Arial; font-size: 10pt; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">bbmap.sh ref=reference.fa in=reads.fq outm=mapped.fq outu=unmapped.fq</span></div>
<div>
<span style="background-color: transparent; color: #333333; font-family: Arial; font-size: 10pt; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Source: <a href="https://www.biostars.org/p/127992/">https://www.biostars.org/p/127992/</a> Brian Bushnell</span></div>
Kevinhttp://www.blogger.com/profile/02104000187284303966noreply@blogger.com0tag:blogger.com,1999:blog-8959227089815463704.post-91249624176629423092017-04-12T13:55:00.000+08:002017-04-12T13:55:04.784+08:00Control a fleet of embedded unix systems (eg Raspberry Pi, Orange Pi) using saltstack HAHAHA I share the same name as a software project. Bizarre discovery today <br />
<a href="https://www.blogger.com/goog_1960360506"><br /></a>
<a href="https://github.com/unixbigot/kevin">https://github.com/unixbigot/kevin</a><br />
<span class="col-11 text-gray-dark mr-2" itemprop="about">Control a fleet of embedded unix systems (eg Raspberry Pi, Orange Pi) using saltstack
</span>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-8959227089815463704.post-54311759082658561822017-04-11T11:21:00.000+08:002017-04-11T11:21:11.223+08:00github-based, community-maintained list of cancer clinical informatics resources<br />
<span class="ember-view" id="ember6613" style="-webkit-text-stroke-width: 0px; background: 0px 0px rgb(255, 255, 255); border: 0px; box-sizing: inherit; color: rgba(0, 0, 0, 0.701961); font-family: "Source Sans Pro", Helvetica, Arial, sans-serif, "Hiragino Kaku Gothic Pro", Meiryo, "Hiragino Sans GB W3", "Noto Naskh Arabic", "Droid Arabic Naskh", "Geeza Pro", "Simplified Arabic", "Noto Sans Thai", Thonburi, Dokchampa, "Droid Sans Thai", "Droid Sans Fallback", -apple-system, ".SFNSDisplay-Regular", "Heiti SC", "Microsoft Yahei", "Segoe UI"; font-size: 15px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: normal; letter-spacing: normal; margin: 0px; orphans: 2; outline: 0px; padding: 0px; text-align: left; text-decoration-color: initial; text-decoration-style: initial; text-indent: 0px; text-transform: none; vertical-align: baseline; white-space: pre-wrap; widows: 2; word-spacing: 0px;"><span style="background: 0px 0px; border: 0px; box-sizing: inherit; font-size: 15px; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Sean Davis created a github-based, community-maintained list of cancer clinical informatics resources. </span></span><br />
<span class="ember-view" id="ember6613" style="-webkit-text-stroke-width: 0px; background: 0px 0px rgb(255, 255, 255); border: 0px; box-sizing: inherit; color: rgba(0, 0, 0, 0.701961); font-family: "Source Sans Pro", Helvetica, Arial, sans-serif, "Hiragino Kaku Gothic Pro", Meiryo, "Hiragino Sans GB W3", "Noto Naskh Arabic", "Droid Arabic Naskh", "Geeza Pro", "Simplified Arabic", "Noto Sans Thai", Thonburi, Dokchampa, "Droid Sans Thai", "Droid Sans Fallback", -apple-system, ".SFNSDisplay-Regular", "Heiti SC", "Microsoft Yahei", "Segoe UI"; font-size: 15px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: normal; letter-spacing: normal; margin: 0px; orphans: 2; outline: 0px; padding: 0px; text-align: left; text-decoration-color: initial; text-decoration-style: initial; text-indent: 0px; text-transform: none; vertical-align: baseline; white-space: pre-wrap; widows: 2; word-spacing: 0px;"><span style="background: 0px 0px; border: 0px; box-sizing: inherit; font-size: 15px; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">"Contributions are welcome!"
</span></span><a class="feed-link ember-view" href="https://lnkd.in/d-uphUc" id="ember6616" style="-webkit-text-stroke-width: 0px; background: 0px 0px rgb(255, 255, 255); border: 0px; box-sizing: inherit; color: #827be9; font-family: "Source Sans Pro", Helvetica, Arial, sans-serif, "Hiragino Kaku Gothic Pro", Meiryo, "Hiragino Sans GB W3", "Noto Naskh Arabic", "Droid Arabic Naskh", "Geeza Pro", "Simplified Arabic", "Noto Sans Thai", Thonburi, Dokchampa, "Droid Sans Thai", "Droid Sans Fallback", -apple-system, ".SFNSDisplay-Regular", "Heiti SC", "Microsoft Yahei", "Segoe UI"; font-size: 15px; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 700; letter-spacing: normal; margin: 0px; orphans: 2; padding: 0px; text-align: left; text-decoration: none; text-indent: 0px; text-transform: none; touch-action: manipulation; vertical-align: baseline; white-space: pre-wrap; widows: 2; word-spacing: 0px;" target="_blank">https://lnkd.in/d-uphUc</a><br />
<br />
For now, it's named as <br />
<div style="-webkit-text-stroke-width: 0px; border-bottom: 1px solid rgb(234, 236, 239); box-sizing: border-box; color: #24292e; font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Helvetica, Arial, sans-serif, "Apple Color Emoji", "Segoe UI Emoji", "Segoe UI Symbol"; font-size: 2em; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 600; letter-spacing: normal; line-height: 1.25; margin-bottom: 16px; margin-left: 0px; margin-right: 0px; margin-top: 0px !important; orphans: 2; padding-bottom: 0.3em; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;">
<span style="font-size: small;"><span style="font-weight: normal;">ci4cc-informatics-resources </span></span></div>
<div style="-webkit-text-stroke-width: 0px; border-bottom: 1px solid rgb(234, 236, 239); box-sizing: border-box; color: #24292e; font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Helvetica, Arial, sans-serif, "Apple Color Emoji", "Segoe UI Emoji", "Segoe UI Symbol"; font-size: 2em; font-style: normal; font-variant-caps: normal; font-variant-ligatures: normal; font-weight: 600; letter-spacing: normal; line-height: 1.25; margin-bottom: 16px; margin-left: 0px; margin-right: 0px; margin-top: 0px !important; orphans: 2; padding-bottom: 0.3em; text-align: start; text-decoration-color: initial; text-decoration-style: initial; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;">
<span style="font-size: small;"><span style="font-weight: normal;"><a href="https://github.com/seandavi/ci4cc-informatics-resources">https://github.com/seandavi/ci4cc-informatics-resources</a> </span></span></div>
Unknownnoreply@blogger.com0