[Biopython] [bip] ngs_backbone

[Steve Lianoglou]

Hi,

In addition to to ngs_backgone and HTseq, people might be interested
in the Genomedata package being developed at the university of
washington:

http://noble.gs.washington.edu/proj/genomedata/

I haven't used it myself, but I've been meaning to check it out.
On Wed, May 5, 2010 at 9:04 AM, Brad Chapman <chapmanb at 50mail.com> wrote:
> Jose;
> (cc'ing in the bip list and Simon)
>
>> As in many other labs we are working with NGS sequences. We work mostly in non
>> model plants and we were repeating the same analyses for different projects:
>> sequence cleaning, mapping to a reference, annotation and SNV calling and
>> filtering. To solve the problem we have developed a software named
>> ngs_backbone. We use this software and we think that it might be of some use
>> to the biopython community. To take a look at it you can go to
>> http://bioinf.comav.upv.es/ngs_backbone/index.html
>
> This looks nice and will be really useful to the Python community.
> I'll take a more in-depth look, and wanted to point out Simon
> Ander's HTSeq project which was announced a week ago:
>
> http://www-huber.embl.de/users/anders/HTSeq/
>
> You are both attacking an overlapping set of problems. One thing
> I've learned in developing infrastructure and pipelines is that it
> is never very general until a lot of people are using it; ideas that
> are intuitive to one set of developers will be totally inscrutable
> show stoppers to another.
>
> This is definitely a space where Python works well, and it would be
> cool to see a unified effort for developing these that reuses
> Biopython, pygr, bx-python, PyCogent and friends on the backend.
>
> Brad
>
> _______________________________________________
> biology-in-python mailing list - bip at lists.idyll.org.
>
> See http://bio.scipy.org/ for our Wiki.
>



-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact