As mentioned by Keith, sequencing by hybridisation isn't a novel idea in fact i thought that was the technology that might speed up sequencing by orders of magnitude of n where n is the length of your oligos.
However, what's interesting about nanostring is that their tech uses no enzymes in the sequencing process.
It's still in early stages of development, shall keep my eyes peeled on them. Maybe they might grow big enough for a sequencing company to consider suing them as well.
Hope over to Omics! for a more extensive write-up
Showing posts with label sequencing. Show all posts
Showing posts with label sequencing. Show all posts
Friday, 26 February 2016
Wednesday, 24 July 2013
Illumina produces 3k of 8500 bp reads on HiSeq using Moleculo Technology
Keith blogged about how super long read sequencing methods would be a threat to Illumina in Jan 2013. Today, Illumina can now openly acknowledge the shortcomings of their short reads for various applications like
the reason?
This latest set of data released on BaseSpace
image source: http://blog.basespace.illumina.com/2013/07/22/first-data-set-from-fasttrack-long-reads-early-access-service/
with the integration of Moleculo they have managed to generate ~30 gb of raw sequence data. They have refrained from talking about 'key analysis metrics' that's available in the pdf report. Perhaps it's much easier to let the blogosphere and data scientists dissect the new data themselves.
Am wondering when the 454 versus Illumina Long Reads side-by-side comparison will pop up
so please update me if you see it otherwise I just have to run something on it
These are the files that I have now
total 512M
259M Jul 18 01:01 mol-32-2832.fastq.gz
44K Jul 24 2013 FastTrackLongReads_dmelanogaster_281c.pdf
149K Jul 24 2013 mol-32-281c-scaffolds.txt
44K Jul 24 2013 FastTrackLongReads_dmelanogaster_2832.pdf
151K Jul 24 2013 mol-32-2832-scaffolds.txt
253M Jul 24 2013 mol-32-281c.fastq.gz
md5sums
6845fc3a4da9f93efc3a52f288e2d7a0 FastTrackLongReads_dmelanogaster_281c.pdf
02f5de4f7e15bbcd96ada6e78f659fdb FastTrackLongReads_dmelanogaster_2832.pdf
586599bb7fca3c20ba82a82921e8ba3f mol-32-281c-scaffolds.txt
b25010e9e5e13dc7befc43b5dff8c3d6 mol-32-281c.fastq.gz
6822cfbd3eb2a535a38a5022c1d3c336 mol-32-2832-scaffolds.txt
873f09080cdf59ed37b3676cddcbe26f mol-32-2832.fastq.gz
I have ran FastQC (FastQC v0.10.1) on both samples the images below are from 281c.
you can download the full HTML report here
https://www.dropbox.com/sh/5unu3zba9u21ywj/JT4HdkzfOP/mol-32-281c_fastqc.zip
https://www.dropbox.com/s/mpxa5wx51iqmiz3/mol-32-2832_fastqc.zip
Reading about the Moleculo sample prep method, it seems like it's just a rather ingenious way to stitch short reads which are barcoded to form a single long contig. if that is the case, then I am not sure if the base quality scores here are meaningful anymore since it's a mini-assembly. Also this takes out any quantitative value of the number of reads I presume. So accurate quantification of long RNA molecules or splice variants isn't possible. Nevertheless it's an interesting development on the Illumina platform. Looking forward to seeing more news about it.
Moleculo technology: synthetic long reads for genome phasing, de novo sequencing
CoreGenomics: Genome partitioning: my moleculo-esque idea
Moleculo and Haplotype Phasing - The Next Generation TechnologistNext Generation Technologist
Abstract: Production Of Long (1.5kb – 15.0kb), Accurate, DNA Sequencing Reads Using An Illumina HiSeq2000 To Support De Novo Assembly Of The Blue Catfish Genome (Plant and Animal Genome XXI Conference)
http://www.moleculo.com/ (no info on this page though)
Illumina Announces Phasing Analysis Service for Human Whole-Genome Sequencing - MarketWatch
https://docs.google.com/viewer?url=patentimages.storage.googleapis.com/pdfs/US20130079231.pdf
- assembly of complex genomes (polyploid, containing excessive long repeat regions, etc.),
- accurate transcript assembly,
- metagenomics of complex communities,
- and phasing of long haplotype blocks.
the reason?
This latest set of data released on BaseSpace
 |
| Read length distribution of synthetic long reads for a D. melanogaster library |
The data set, available as a single project in BaseSpace, can be accessed here.
image source: http://blog.basespace.illumina.com/2013/07/22/first-data-set-from-fasttrack-long-reads-early-access-service/
with the integration of Moleculo they have managed to generate ~30 gb of raw sequence data. They have refrained from talking about 'key analysis metrics' that's available in the pdf report. Perhaps it's much easier to let the blogosphere and data scientists dissect the new data themselves.
Am wondering when the 454 versus Illumina Long Reads side-by-side comparison will pop up
UPDATE:
Can't find the 'key analysis metrics' in the pdf report files. Perhaps it's still being uploaded? *shrugs*so please update me if you see it otherwise I just have to run something on it
These are the files that I have now
total 512M
259M Jul 18 01:01 mol-32-2832.fastq.gz
44K Jul 24 2013 FastTrackLongReads_dmelanogaster_281c.pdf
149K Jul 24 2013 mol-32-281c-scaffolds.txt
44K Jul 24 2013 FastTrackLongReads_dmelanogaster_2832.pdf
151K Jul 24 2013 mol-32-2832-scaffolds.txt
253M Jul 24 2013 mol-32-281c.fastq.gz
md5sums
6845fc3a4da9f93efc3a52f288e2d7a0 FastTrackLongReads_dmelanogaster_281c.pdf
02f5de4f7e15bbcd96ada6e78f659fdb FastTrackLongReads_dmelanogaster_2832.pdf
586599bb7fca3c20ba82a82921e8ba3f mol-32-281c-scaffolds.txt
b25010e9e5e13dc7befc43b5dff8c3d6 mol-32-281c.fastq.gz
6822cfbd3eb2a535a38a5022c1d3c336 mol-32-2832-scaffolds.txt
873f09080cdf59ed37b3676cddcbe26f mol-32-2832.fastq.gz
I have ran FastQC (FastQC v0.10.1) on both samples the images below are from 281c.
you can download the full HTML report here
https://www.dropbox.com/sh/5unu3zba9u21ywj/JT4HdkzfOP/mol-32-281c_fastqc.zip
https://www.dropbox.com/s/mpxa5wx51iqmiz3/mol-32-2832_fastqc.zip
Reading about the Moleculo sample prep method, it seems like it's just a rather ingenious way to stitch short reads which are barcoded to form a single long contig. if that is the case, then I am not sure if the base quality scores here are meaningful anymore since it's a mini-assembly. Also this takes out any quantitative value of the number of reads I presume. So accurate quantification of long RNA molecules or splice variants isn't possible. Nevertheless it's an interesting development on the Illumina platform. Looking forward to seeing more news about it.
Other links
Illumina Long-Read Sequencing ServiceMoleculo technology: synthetic long reads for genome phasing, de novo sequencing
CoreGenomics: Genome partitioning: my moleculo-esque idea
Moleculo and Haplotype Phasing - The Next Generation TechnologistNext Generation Technologist
Abstract: Production Of Long (1.5kb – 15.0kb), Accurate, DNA Sequencing Reads Using An Illumina HiSeq2000 To Support De Novo Assembly Of The Blue Catfish Genome (Plant and Animal Genome XXI Conference)
http://www.moleculo.com/ (no info on this page though)
Illumina Announces Phasing Analysis Service for Human Whole-Genome Sequencing - MarketWatch
Illumina Announces Moleculo Long Read Technology and Phasing As Service
First publication using the Long Read Seq (LRseq) The genome sequence of the colonial chordate, Botryllus schlosseri | eLife Contains a diagram explaining the LRSeq protocol. This experiment yielded ~1000 6.3kb fragments
Patent information on the Long Read technologyFirst publication using the Long Read Seq (LRseq) The genome sequence of the colonial chordate, Botryllus schlosseri | eLife Contains a diagram explaining the LRSeq protocol. This experiment yielded ~1000 6.3kb fragments
https://docs.google.com/viewer?url=patentimages.storage.googleapis.com/pdfs/US20130079231.pdf
Tuesday, 15 May 2012
NATURE BIOTECHNOLOGY | Performance comparison of benchtop high-throughput sequencing platforms
NATURE BIOTECHNOLOGY | RESEARCH | ANALYSIS
Performance comparison of benchtop high-throughput sequencing platforms
- Nature Biotechnology
- 30,
- 434–439
- (2012)
- doi:10.1038/nbt.2198
Tuesday, 6 December 2011
I can imagine personal genomes being shipped in these : SanDisk(R) Memory Vault
Chanced upon this SSD with an interesting feature that states that it can support data retention up to 100 years. Perhaps in the future, we might get our genome sequences saved in one of this.(two just for redundancy). You might be sequenced at birth and this info is used for all your medical consultations to receive personalized medicine / consultation throughout your lifetime ...
http://www.sandisk.com/products/memory-vault/sandisk-memory-vault
Introducing the SanDisk Memory Vault, the first product from SanDisk engineered to preserve your most important photos, videos, documents, and scanned files for generations to come.
SanDisk Memory Vault features Chronolock™ technology:
For the details on the testing methods ...
http://www.sandisk.com/misc/preserve
The Arrhenius equation expresses the relationship between the rate constant (or acceleration factor) and the activation energy and temperature of a reaction.
Figure 1. Arrhenius Equation
EXAMPLE: The following example is for illustrative purposes
only. Actual figures used to validate data retention properties
meet and or exceed standard product usage parameters. In this
example, the test calculation the following temperatures and
activation energies were used:
kevin:Not affliated with them but won't mind a tester unit from them!
http://www.sandisk.com/products/memory-vault/sandisk-memory-vault
Introducing the SanDisk Memory Vault, the first product from SanDisk engineered to preserve your most important photos, videos, documents, and scanned files for generations to come.
SanDisk Memory Vault features Chronolock™ technology:
- Engineered to preserve the quality of photos and videos long term
- Tested to support data retention for up to 100 years*
- Physically designed for long-term reliability and durability
For the details on the testing methods ...
http://www.sandisk.com/misc/preserve
Data Retention Test Methodology
In order substantiate show how SanDisk Memory Vault technology can support 100 year data retention, accelerated temperature cycling and the Arrhenius acceleration factor was used to simulate the effects to data retention over long durations of memory usage.The Arrhenius equation expresses the relationship between the rate constant (or acceleration factor) and the activation energy and temperature of a reaction.
Figure 1. Arrhenius Equation
- Ea = Activation Energy = 1.0 ev
- Boltzmann Constant = 8.62*10-5
- Product application temperature used for this test (Ta) = 35ºC
- Product test temperature used for this test (Tt) = 125ºC
- Product's time-to-failure is exponential
kevin:Not affliated with them but won't mind a tester unit from them!
Wednesday, 2 March 2011
Papers on Comparison of microRNA profiling platforms
Systematic Evaluation of Three microRNA Profiling Platforms: Microarray, Beads Array, and Quantitative Real-Time PCR Array
Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential microRNA expression
Abstract
RNA abundance and DNA copy number are routinely measured in high-throughput using microarray and next-generation sequencing (NGS) technologies, and the attributes of different platforms have been extensively analyzed. Recently, the application of both microarrays and NGS has expanded to include microRNAs (miRNAs), but the relative performance of these methods has not been rigorously characterized. We analyzed three biological samples across six miRNA microarray platforms and compared their hybridization performance. We examined the utility of these platforms, as well as NGS, for the detection of differentially expressed miRNAs. We then validated the results for 89 miRNAs by real-time RT-PCR and challenged the use of this assay as a “gold standard.” Finally, we implemented a novel method to evaluate false-positive and false-negative rates for all methods in the absence of a reference method.
Background
A number of gene-profiling methodologies have been applied to microRNA research. The diversity of the platforms and analytical methods makes the comparison and integration of cross-platform microRNA profiling data challenging. In this study, we systematically analyze three representative microRNA profiling platforms: Locked Nucleic Acid (LNA) microarray, beads array, and TaqMan quantitative real-time PCR Low Density Array (TLDA).
Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential microRNA expression
Abstract
RNA abundance and DNA copy number are routinely measured in high-throughput using microarray and next-generation sequencing (NGS) technologies, and the attributes of different platforms have been extensively analyzed. Recently, the application of both microarrays and NGS has expanded to include microRNAs (miRNAs), but the relative performance of these methods has not been rigorously characterized. We analyzed three biological samples across six miRNA microarray platforms and compared their hybridization performance. We examined the utility of these platforms, as well as NGS, for the detection of differentially expressed miRNAs. We then validated the results for 89 miRNAs by real-time RT-PCR and challenged the use of this assay as a “gold standard.” Finally, we implemented a novel method to evaluate false-positive and false-negative rates for all methods in the absence of a reference method.
Tuesday, 1 December 2009
New Job new distro
Have started in a new job!
but basically am doing Next Generation Sequencing Bioinformatics.
Sounds like a mouthful but hope it goes well.
1st week was spent on sourcing a cheap cluster for analysis. but 'cheap cluster' is an oxymoron!
Playing around with CentOS now. So far, its less than enjoyable compared to Ubuntu. Especially the 7 CDs or single DVD downloading.
I can't understand why making people download so many RPMs would be a good thing for bandwidth or convenience.
I miss my Ubuntu box. but setting up a HPC cluster using Ubuntu might be tricky without tech support.
Any advice for those familiar with ABI Solid's offline cluster setup?
but basically am doing Next Generation Sequencing Bioinformatics.
Sounds like a mouthful but hope it goes well.
1st week was spent on sourcing a cheap cluster for analysis. but 'cheap cluster' is an oxymoron!
Playing around with CentOS now. So far, its less than enjoyable compared to Ubuntu. Especially the 7 CDs or single DVD downloading.
I can't understand why making people download so many RPMs would be a good thing for bandwidth or convenience.
I miss my Ubuntu box. but setting up a HPC cluster using Ubuntu might be tricky without tech support.
Any advice for those familiar with ABI Solid's offline cluster setup?
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