[Bioperl-l] Run wrappers for BWA and Samtools

Albert Vilella avilella at gmail.com
Mon Jul 26 05:08:32 EDT 2010


Hi Mark,

First of all, great work.

Can I ask if the aim of combining bwa and samtools would be or could
be to replicate
"maq.pl easyrun" ?

Or what would be an alternative for users wanting to do "maq.pl
easyrun" for a combination of long and short reads?

Cheers,

Albert.

On Sat, Nov 28, 2009 at 5:23 PM, Mark A. Jensen <maj at fortinbras.us> wrote:
> 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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