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

[Peter Cock]

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.
>
> Sincerely,
> Afiahayati

Hello Afiahayati,

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
SAM: https://github.com/peterjc/maf2sam

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?

Peter