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

Chris Fields cjfields at illinois.edu
Mon Jan 18 22:36:12 EST 2010

On Jan 18, 2010, at 8:47 PM, Dan Kortschak wrote:

> 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

And (on behalf of the core devs) thank you for putting this together!


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