26 April 2013

Java JNI bindings for BWA(mem-lite)

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Motivation BWA 7.4( http://bio-bwa.sourceforge.net/ ) contains a small C example( https://github.com/lh3/bwa/blob/master/example.c ) for r...
4 comments:
23 April 2013

playing with BWA-MEM : my notebook

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BWA-MEM , is a new tool that is part of the latest version of BWA . As said Heng Li on Biostar bwa-mem can be used to identify the viral in...
25 March 2013

Embedding Pubmed, Graphiviz and a remote image in #LaTeX. My notebook. .

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I'm learning LaTeX . Today I learned how to create a new command in LaTeX. \newcommand{name}[num]{definition} "Basically the comm...
1 comment:
13 March 2013

Filtering a BAM with javascript.

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The following was created to answer that question on biostar: " Exclude reads with XA tag ". SamJs is a java program filtering th...
27 February 2013

4 Tools I wrote today to annotate VCF files.

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Here are four java-bases tools I wrote today for @SolenaLS to annotate VCF files. VCFTabix VCFTabix : we want to use the VCF of the 1K...
4 comments:
11 February 2013

Counting the reads in a BAM file using SGE and the Open-MPI library: my notebook.

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In the current post, I'll describe my first Open MPI program. Open MPI is "a Message Passing Interface (MPI) library, a standard...
1 comment:
07 February 2013

A tool to compare the BAMs

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Following that thread on Biostar , I've created a tool that compares two or more BAMs . This java program uses the Picard and berkeleyd...
05 February 2013

Making use of Picard Metrics files using XML and XSLT. #ngs

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Many tools in the Picard package produce some "Metrics File" (described at http://picard.sourceforge.net/picard-metric-definiti...
25 January 2013

Samtools tview as a library to display the BAM

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I've forked samtools and modified the code of tview to use it as a library to display the alignments. The original code is an inreracti...
3 comments:
09 January 2013

A XML schema (xsd) for GeneOntology

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The GeneOntology can be downloaded as a RDF/XML file from http://archive.geneontology.org/latest-termdb/go_daily-termdb.rdf-xml.gz . Althou...