Using Galaxy for NGS sample submission and tracking for service providers

Over at the Blue Collar Bioinformatics 
Our group at Massachusetts General Hospital approached these challenges by developing a sample submission and tracking interface on top of the web-based Galaxy data integration platform. It provides a front end for biologists to enter their sample details and monitor the status of a project. For lab technicians doing the sample preparation and sequencing work, the system tracks sample states via a set of progressive queues providing data entry points at each step of the process. On the back end, an automated analysis pipeline processes data as it arrives off the sequencer, uploading the results back into Galaxy.
This post will show videos of the interface in action, describe installation and extension of the system, and detail the implementation architecture.

RNA-seq of a 12GB dataset in less than 7 hours

Folks at CLCbio have updated the CLC Genomics Machine benchmarks with newer datasets and the new hardware configuration. There are two RNA-Seq data sets and a full genome mapping data set, and more will come. All the benchmarks are now using the CLC Genomics Server rather than the Assembly Cell.

script 4 filter to unique FASTQ reads using a bloom-filter in front of a python set

from the hackmap blog 

a simple script that filters to unique FASTQ reads using a bloom-filter in front of a python set. Basically only stuff that is flagged as appearing in the bloom-filter is added to the set. This trades speed--it iterates over the file 3 times--for memory. The amount of memory is tuneable by the specified error-rate. It's not pretty, but it should be simple enough to demonstrate what's going on. It only reads from stdin and writes to stdout, with some information about total reads an number of false positives in the bloom-filter sent to stderr.
usage looks like:
python fastq-unique.py > in.fastq < out.unique.fastq

Updated overview of NGS and SMS platforms

Range of NGS Applications Rises Quickly

• Vicki Glaser

Advanced Technological Approach Generates Genomic Data Better, Faster, and Cheaper

...

PacBio applied its single molecule real-time (SMRT™) DNA sequencing technology to decode two samples from the recent Haitian outbreak and three other strains of V. cholerae and compared them to DNA sequence....

Key advantages of MiSeq are its fast turnaround time, ease of use, and simple sample prep, said David Bentley, Ph.D. Dr. Bentley, chief scientist at Illumina, envisions customers using the system for various types of applications: to check a small amount of sample before running it on HiSeq, to analyze large numbers of poor-quality DNA samples isolated from FFPE tissues, and to detect specific mutations in patient samples from clinical trial populations.

 

Life Technologies’ Ion Personal Genome Machine (PGM™) is based on Ion Torrent’s semiconductor sequencing chips that translate chemical signals into digital information. The 314 sequencing chip contains an array of 1.3 million wells; each is the site of an individual sequencing reaction. A pH change is detected when incorporation of a new base onto a growing DNA strand produces hydrogen ions.

Complete Genomics, which leverages its human genome sequencing capabilities through a service delivery platform, employs a sequencing method based on DNA nanoball (DNB™) arrays and combinatorial probe-anchor ligation read technology. The company optimized its sequencing technology specifically for the human genome and delivers to its customers annotated sequence data, identifying key sites of sequence variation.

 

Intelligent Bio-Systems’ three-step sequencing-by-synthesis technology involves amplifying DNA fragments, attaching them to a DNA sequence primer, and then immobilizing them in a high-density array on a glass chip. Fluorescently labeled bases (a different color for A, C, G, and T) are then introduced and attach to the growing DNA strand. The array is scanned and the fluorescent signal emitted by each replicating strand indicates with base was incorporated at the completion of each base addition step.

RStudio IDE for R ... looks promising!

RStudio, released yesterday, is a new open-source IDE for R. It’s getting a lot of attention at R-bloggers and it’s easy to see why: this is open-source software development done right.
from 

What You’re Doing Is Rather Desperate

Notes from the life of a bioinformatics researcher

The Tea Transcriptome

The Tea Transcriptome

from RNA-Seq Blog by admin

Tea is one of the most popular non-alcoholic beverages worldwide. However, the tea plant, Camellia sinensis, is difficult to culture in vitro, to transform, and has a large genome, rendering little genomic information available. Recent advances in large-scale RNA sequencing (RNA-seq) provide a fast, cost-effective, and reliable approach to generate large expression datasets for functional genomic analysis, which is especially suitable for non-model species with un-sequenced genomes. Using high-throughput Illumina RNA-seq, the transcriptome from C. sinensis was analyzed at an unprecedented depth.
(read more… )
Shi C et al. (2011) Deep sequencing of the Camellia sinensis transcriptome revealed candidate genes for major metabolic pathways of tea-specific compounds. BMC Genomics [Epub ahead of print]. [article]
The Tea Transcriptome is a post from: RNA-Seq Blog More information about RNA-Seq can be here.

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons [RESOURCES]

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons [RESOURCES]

from Genome Research current issue by Haas, B. J., Gevers, D., Earl, A. M., Feldgarden, M., Ward, D. V., Giannoukos, G., Ciulla, D., Tabbaa, D., Highlander, S. K., Sodergren, E., Methe, B., DeSantis, T. Z., The Human Microbiome Consortium, Petrosino, J. F., Knight, R., Birren, B. W.

Bacterial diversity among environmental samples is commonly assessed with PCR-amplified 16S rRNA gene (16S) sequences. Perceived diversity, however, can be influenced by sample preparation, primer selection, and formation of chimeric 16S amplification products. Chimeras are hybrid products between multiple parent sequences that can be falsely interpreted as novel organisms, thus inflating apparent diversity. We developed a new chimera detection tool called Chimera Slayer (CS). CS detects chimeras with greater sensitivity than previous methods, performs well on short sequences such as those produced by the 454 Life Sciences (Roche) Genome Sequencer, and can scale to large data sets. By benchmarking CS performance against sequences derived from a controlled DNA mixture of known organisms and a simulated chimera set, we provide insights into the factors that affect chimera formation such as sequence abundance, the extent of similarity between 16S genes, and PCR conditions. Chimeras were found to reproducibly form among independent amplifications and contributed to false perceptions of sample diversity and the false identification of novel taxa, with less-abundant species exhibiting chimera rates exceeding 70%. Shotgun metagenomic sequences of our mock community appear to be devoid of 16S chimeras, supporting a role for shotgun metagenomics in validating novel organisms discovered in targeted sequence surveys.