[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:


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.


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