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

Dan Kortschak dan.kortschak at adelaide.edu.au
Mon Jan 18 21:47:47 EST 2010


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



More information about the Bioperl-l mailing list