[Bioperl-l] Run wrappers for BWA and Samtools

Mark A. Jensen maj at fortinbras.us
Sat Nov 28 11:23:53 EST 2009


Hi All, 

Run wrappers for the bwa assembler and the samtools suite
are now available as beta in the bioperl-run/trunk. The bwa 
wrapper allows you to run a canned assembly pipeline, or 
to execute individual bwa components. The assembly pipeline
can return a Bio::Assembly::Scaffold object via the new 
Bio::Assembly::IO::sam module in bioperl-live/trunk
(this requires lstein's Bio::DB::Sam, from CPAN). Details at

http://www.bioperl.org/wiki/HOWTO:Short-read_assemblies_with_BWA

and, of course, in the pod. 

Cheers, 
MAJ


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