[Biopython-dev] Newbler ACE file to SAM?

[Kevin Jacobs <jacobs@bioinformed.com>]

On Wed, Aug 4, 2010 at 1:24 PM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> On Wed, Aug 4, 2010 at 6:12 PM, Kevin Jacobs wrote:
> > On Wed, Aug 4, 2010 at 1:10 PM, Peter wrote:
> >>
> >> Or ask your Roche representatives to implement SAM/BAM output?
> >> Mind you, as the MIRA3 author has pointed out, SAM/BAM isn't so
> >> great for de novo assemblies. It doesn't even store the contig seq ;)
> >>
> >
> > They're working on it.  :)
> > -Kevin
> >
>
> Do you mean Roche are working on SAM/BAM output? If so, that's good news.



Yes, I believe that Roche is working on SAM/BAM support for a future version
of Newbler.  As of a few weeks ago, when I last spoke to them, they were
just gathering information and had yet to start on the implementation.  I'd
expect to see this feature with Newbler 2.6 (supporting the same features as
2.5 on the FLX, which was for the Jr only) or more likely with the
subsequent  2.7 release.  In other words, I'd be surprised to see it in the
coming weeks or few months.


> If you mean the SAM/BAM format, I'm on the samtools-devel list where
> they are discussing several specification improvements/additions, but
> I don't recall anything specifically aimed at de novo assemblies.
>
>
I didn't see the Roche folks in that discussion, but I'll look again.  As
far as I know, they're not looking to change or alter the spec, but I could
easily be wrong.  I do keep in contact with a few of the folks at Roche, but
have no deep insight into their future plans.

-Kevin