[Bioperl-l] Proposal of GSoC 2012 >> ACEtoSAM and SAMtoACE

Peter Cock p.j.a.cock at googlemail.com
Fri Apr 13 04:32:00 EDT 2012


On Fri, Apr 13, 2012 at 3:41 AM, Florent Angly <florent.angly at gmail.com> wrote:
> Bioperl has a module to read and write ACE files, Bio::Assembly::IO::ace. It
> also has a module to read (but not write) SAM files, Bio::Assembly::IO::sam.
> So, it looks like you can already do SAMtoACE within Bioperl. Implementing
> ACEtoSAM would involve adding write support to the Bio::Assembly::sam
> module. This can be helped by looking at how Bio::Assembly::IO::ace and
> Bio::Assembly::tigr implement write support.
> Regards,
> Florent

Does SAMtoACE within Bioperl using Bio::Assembly::IO actually work?

Note that proper multiple sequence alignments in SAM/BAM format are
relatively rare - the vast majority of SAM/BAM files are just pairwise
alignments which are not a good fit for ACE.

Peter


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