[Bioperl-l] Bio::Tools::Run::Bowtie and Bio::Assembly::IO::bowtie now available BETA

Mark A. Jensen maj at fortinbras.us
Mon Jan 18 22:31:36 EST 2010


Excellent Dan! Thanks for all this work-- MAJ
----- Original Message ----- 
From: "Dan Kortschak" <dan.kortschak at adelaide.edu.au>
To: <bioperl-l at lists.open-bio.org>
Sent: Monday, January 18, 2010 9:47 PM
Subject: [Bioperl-l] Bio::Tools::Run::Bowtie and Bio::Assembly::IO::bowtie now 
available BETA


> Hi All,
>
> A wrapper and output parser for bowtie 'ultrafast, memory-efficient
> short read aligner' are now available in the bioperl-live and
> bioperl-run subversion repositories (bioperl-live/trunk at 16727 and
> bioperl-run/trunk at 16726). Bowtie details are available here:
>
> http://bowtie-bio.sourceforge.net/index.shtml
>
> The modules can return a Bio::Assembly::Scaffold object (operating via
> the MAJ's Bio::Assembly::IO::sam module in bioperl-live/trunk
> which requires lstein's Bio::DB::Sam, from CPAN). Note that Bio::DB::Sam
> uses large amounts of memory - the test suite works for me with >=2GB
> but not with 1GB due to this. (Is there a disk file system based tool
> for this for large projects?)
>
> Bowtie (>0.12.0) can align in colour space, but this is not currently
> supported by the wrapper though it should not be difficult to add. If
> someone can point me to a small set of colour space reads and a
> reference sequence I will be able to use these for testing.
>
> Thanks to the core devs for helping me with many of my problems in
> putting this together.
>
> Dan
>
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