GNU parallel for Bioinformatics: my notebook

<p>This tutorial follows<strong> Ole Tange</strong>’s GNU parallel tutorial ( http://www.gnu.org/software/parallel/parallel_tutorial.html ) but I tried to use some bioinformatics-related  examples (align with BWA, Samtools, etc.. ).</p> <p> </p

JVarkit: java-based utilities for Bioinformatics

<p>This article is a placeholder to get a reference for <strong>Jvarkit</strong> ( https://github.com/lindenb/jvarkit ), a set<br>of more than 100 java-based tools for bioinformatics I’ve written during the last years.</p> <p> </p

RoXaN, une nouvelle protéine cellulaire interagissant avec la protéine non-structurale NSP3 du Rotavirus.CloneIt: Un programme en ligne trouvant des stratégies de clonage.

<p>we characterized a new cellular protein called<br>RoXaN (Rotavirus X associated Non structural protein) and  showed that it interacts specifically with<br>NSP3</p> <p> </p> <p>CloneItTM finds strategies of sub-cloning, in frame deletions and frameshifts by<br>using restriction enzymes and DNA polymerases.</p> <p> </p> <p> </p

"Mon make à moi" Everything but #usegalaxy

<p>My talk at ReNaBI-Grand Ouest, Nov. 2013. Conference about workflows & bioinformatics.</p

RDF/Jena : an extension for XSLT/Xalan. Testing with NCBI gene and the disease ontology.

<p>The current code contains an extension for the XSLT processor apache XALAN : it allows to search and inject some RDF statements during a XSLT transformation. As an example, the makefile transforms a NCBI-gene record to HTML and annotate it with the disease-ontology .</p

PrettySam : a SAM /BAM prettifier.

’<b>Prettysam</b>’ is a SAM /BAM prettifier. It displays the de-<br>tails about the short-reads when they’re viewed through a terminal

Vcf2table : a VCF prettifier.

’<b>vcf2table</b>’ ’vcf2table’ is a Variant Call Format (VCF) prettyfier. It displays the details of the variants as a set of ASCII tables when they’re viewed through a terminal

XML4NGS : A XML-based description of a Next-Generation sequencing project allowing the generation of a ’Makefile’-driven workflow.

<p>[in french] Poster presented at JOBIM2013 https://colloque.inra.fr/jobim2013/layout/set/print/Soumission2/Liste-des-soumissions-retenues-pour-une-presentation-sous-forme-d-affiche</p> <p>XML4NGS is a schema describing a NGS experiment in XML. It provides a XSLT<br>stylesheet transforming the XML into a Makefile-driven workflow allowing a parallel analysis<br>(alignment, calling, annotation ... ) on a cluster.</p> <p> </p> <p> </p