[Biopython-dev] Command line wrappers for assembly tools

[Peter]

Hi all,

Osvaldo Zagordi has recently offered a Bio.Application style command line
wrapper for Novoalign (a commercial short read aligner from Novocraft), see
enhancement Bug 2904, and the Novocraft website:
http://bugzilla.open-bio.org/show_bug.cgi?id=2904
http://www.novocraft.com/products.html

Note that Novocraft do offer a trial/evaluation version, but I have no idea
what the terms and conditions are, and I personally do not have access
to the commercial tool (e.g. for testing the wrapper). Nevertheless, this
would be a nice addition to Biopython.

I personally would like to have wrappers for some of the "off instrument"
applications from Roche 454 (e.g. the Newbler assembler, read mapper
and perhaps their SFF tools), which I have been using. These are Linux
only (which is a pain as Windows and Mac OS X are out), but Roche
seem relatively relaxed about making the software available to any
academics using their sequencer (I'd suggest anyone interested
contact your local sequencing centre for this).

While some of these tools would fit under Bio.Align.Applications, does
creating a similar collection at Bio.Sequencing.Applications make more
sense? For example, the Roche sffinfo tool isn't in itself a alignment
application - but it is related to DNA sequencing.

Peter