[Biopython] ngs_backbone

[Brad Chapman]

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