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

Dan Kortschak dan.kortschak at adelaide.edu.au
Tue Jan 19 16:18:20 EST 2010


Great.

Thanks, Scott.

Dan

On Tue, 2010-01-19 at 10:00 -0800, Scott Markel wrote:
> Dan,
> 
> Life Tech has sample data for E. coli at
> 
> http://solidsoftwaretools.com/gf/project/ecoli2x50/
> 
> and
> 
> http://solidsoftwaretools.com/gf/project/dh10bfrag/.
> 
> Reference sequences are included.
> 
> Scott
> 
> Scott Markel, Ph.D.
> Principal Bioinformatics Architect  email:  smarkel at accelrys.com
> Accelrys (Pipeline Pilot R&D)       mobile: +1 858 205 3653
> 10188 Telesis Court, Suite 100      voice:  +1 858 799 5603
> San Diego, CA 92121                 fax:    +1 858 799 5222
> USA                                 web:    http://www.accelrys.com
> 
> http://www.linkedin.com/in/smarkel
> Vice President, Board of Directors:
>     International Society for Computational Biology
> Chair: ISCB Publications Committee
> Associate Editor: PLoS Computational Biology
> Editorial Board: Briefings in Bioinformatics
> 
> 
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Dan Kortschak
> Sent: Monday, 18 January 2010 6:48 PM
> To: bioperl-l at lists.open-bio.org
> 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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