29 June 2015

A BLAST to SAM converter.

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Some times ago, I've received a set of Ion-Torrent /mate-reads with a poor quality. I wasn't able to align much things using bwa. I...
8 comments:
18 June 2015

Playing with the #GA4GH schemas and #Avro : my notebook

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After watching David Haussler's talk "Beacon Project and Data Sharing ApIs" , I wanted to play with Avro and the models and ...
07 May 2015

Monitoring a java application with mbeans. An example with samtools/htsjdk.

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"A MBean is a Java object that follows the JMX specification. A MBean can represent a device, an application, or any resource that nee...
05 May 2015

Playing with hadoop/mapreduce and htsjdk/VCF : my notebook.

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The aim of this test is to get a count of each type of variant/genotypes in a VCF file using Apache Hadoop and the java library for NGS ht...
1 comment:
28 February 2015

Integrating a java program in #usegalaxy.

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This is my notebook for the integration of java programs in https://usegalaxy.org/ . create a directory for your tools under ${galaxy-roo...
22 February 2015

Drawing a Manhattan plot in SVG using a GWAS+XML model.

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On friday, I saw my colleague @b_l_k starting writing SVG +XML code to draw a Manhattan plot . I told him that a better idea would be to ...
18 February 2015

Automatic code generation for @knime with XSLT: An example with two nodes: fasta reader and writer.

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KNIME is a java+eclipse-based graphical workflow-manager. Biologists in my lab often use this tool to filter VCFs or other tabular data....
02 February 2015

Listing the 'Subject' Sequences in a BLAST database using the NCBI C++ toolbox. My notebook.

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In my previous post ( http://plindenbaum.blogspot.com/2015/01/filtering-fasta-sequences-using-ncbi-c.html ) I've built an application fi...
2 comments: