[Bioperl-l] Proposal of GSoC 2012 >> ACEtoSAM and SAMtoACE
p.j.a.cock at googlemail.com
Thu Apr 12 08:47:05 EDT 2012
On Thu, Apr 5, 2012 at 5:52 AM, afia hayati <afia.hayati at gmail.com> wrote:
> Dear all,
> I am afia, a PhD student in Bioinformatics. I am so interested to
> participate GSoC and would like to apply for project Bio::Assembly, Ace2Sam
> and Sam2Ace converter. I have written a proposal based on the guidance for
> prospective GSoC student. I paste my proposal in here.
> If you have time, please give me suggestions.
> Thank you very much.
What would you use this converter for?
I can see it is useful to convert ACE to SAM/BAM for downstream analysis
and visualization. At the moment the only assemblers I regularly use which
produce ACE are the Roche 'Newbler' gsAssember, and MIRA.
For MIRA, Bastien is working on native SAM output, but for the moment
I wrote and maintain a converter from MIRA's alignment format (MAF) to
Or is the idea more to support SAM (and BAM) assemblies within the
existing BioPerl Bio::Assembly::IO: framework to allow easier
manipulation from Perl?
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