[Biopython-dev] Newbler ACE file to SAM?

[Kevin Jacobs <jacobs@bioinformed.com>]

On Wed, Aug 4, 2010 at 4:41 PM, Kevin Jacobs <jacobs at bioinformed.com> <
bioinformed at gmail.com> wrote:

> On Wed, Aug 4, 2010 at 12:32 PM, Nick Loman <n.j.loman at bham.ac.uk> wrote:
>
>> I'm pretty sure the ACE files contain the individual reads (or at the
>> least, the trimmed, aligned portions of them) because this is the file one
>> uses in Consed/Tablet to view an assembly. We may of course be talking at
>> cross-purposes!
>>
>>
> I've reviewed the Newbler ACE files and re-discovered the reason why they
> weren't ideal in the first place:
>

Never mind-- I didn't realized the consensus sequence was gapped, so it is
then trivial to recover the original pairwise alignments.  I'll have a
version of my Newbler2SAM module that can process ACE files shortly.

-Kevin