[Biopython-dev] Command line wrappers for assembly tools

[Brad Chapman]

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

Very nice. I've been meaning to play with Novoalign and have heard
some good things.

> 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.

I like the idea of a Sequencing namespace or at least something
different than the current Align, which implicitly refers mostly to
multiple alignment programs.

Brad