12 December 2013

Inside Jvarkit: view BAM, cut, stats, head, tail, shuffle, downsample, group-by-gene VCFs...

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Here are a few tools I recently wrote (and reinvented) for Jvarkit . BamViewGui a simple java-Swing-based BAM viewer. VcfShuffle Shuff...
2 comments:
20 November 2013

Inside Jvarkit: Shrink your fastqs by 40% by aligning them to REF before compression.

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BamToFastq is an implementation of https://twitter.com/DNAntonie/status/402909852277932032 " Shrink your FASTQ.bz2 files by 40+% using...
2 comments:
30 October 2013

GNU Make: saving the versions of the tools using 'order-only-prerequisites' : my notebook

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Rule 3 of "Ten Simple Rules for Reproducible Computational Research" . is : Archive the Exact Versions of All External Programs U...
1 comment:
25 October 2013

YES: "Choice of transcripts and software has a large effect on variant annotation"

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This post was inspired by Aaron Quinlan 's tweet: Poster 1485: variant annotation is harder than you think. transcript set matters (sur...
24 October 2013

PubMed Commons & Bioinformatics: a call for action

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NCBI pubmed Commons / @PubMedCommons is a new system that enables researchers to share their opinions about scientific publications. Resear...
1 comment:
23 October 2013

Inside the variation toolkit: Generating a structured document describing an Illumina directory.

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I wrote a tool named " Illuminadir " : it creates a structured ( JSON or XML ) representation of a directory containing som...
17 October 2013

Rapid prototyping of a read-only Lims using JSON and Apache Velocity.

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In a previous post , I showed how to use the Apache Velocity template engine to format JSON data. Since that post, I've moved my a...
15 October 2013

GNU parallel for #bioinformatics : my notebook

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This notebook about GNU parallel follows Ole Tange’s GNU parallel tutorial ( http://www.gnu.org/software/parallel/parallel_tutorial.html ...
07 October 2013

Software Environment Management with Modules: my notebook

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The following question was recently asked on Biostar " Bioinformatics: how to version control small scripts located all over the serve...
1 comment:
26 September 2013

Presentation : File formats for Next Generation Sequencing

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Here is my presentation for the course " File formats for Next Generation Sequencing ", I gave monday at the University of Nantes....