[Bioperl-l] Bio::Tools::Run::Bowtie and Bio::Assembly::IO::bowtie now available BETA
Scott Markel
SMarkel at accelrys.com
Tue Jan 19 18:00:22 UTC 2010
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
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Vice President, Board of Directors:
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-----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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