[Biopython-dev] Newbler ACE file to SAM?

[Nick Loman]

Kevin Jacobs <jacobs at bioinformed.com> wrote:
> 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.
Hi Kevin

I was wondering how you got on with the ACE to SAM converter?

I now realise that the 454PairAlign.txt produced by Newbler when run in 
de novo assembly mode is not much use to me, as the alignments reported 
in this file are strictly pairwise between reads and don't relate back 
to the assembled contigs. So an ACE file parser would be extremely 
helpful at this point.

Cheers

Nick.