[Biopython-dev] Command line wrappers for assembly tools

[Peter]

On Mon, Aug 31, 2009 at 1:58 PM, Brad Chapman<chapmanb at 50mail.com> wrote:
> 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.

Cool. Do you think you'll be able to try that out, and test Osvaldo's
wrapper at the same time?

>> 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.

That sounds like a plan then...

Peter