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

Scott Markel SMarkel at accelrys.com
Tue Jan 19 13:00:22 EST 2010


Life Tech has sample data for E. coli at




Reference sequences are included.


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

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:


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.


Bioperl-l mailing list
Bioperl-l at lists.open-bio.org

More information about the Bioperl-l mailing list