[Biopython-dev] Newbler ACE file to SAM?

[Kevin Jacobs <jacobs@bioinformed.com>]

On Tue, Aug 17, 2010 at 9:59 AM, Nick Loman <n.j.loman at bham.ac.uk> wrote:

> 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.
>
>
Hi Nick,

I'm stuck with the ACE conversion for exactly the same reason.  The
consensus and reads are  gapped for multiple alignments so that there are no
mismatches at all.  I will have to recompute the Smith-Waterman alignments
of each read against the ungapped consensus in order to produce SAM/BAM
output.  I'm surprised that the pairwise alignments for the de novo assembly
are so problematic.  My understanding was they they were pairwise against
the consensus contigs and would be exactly what you'd want for SAM/BAM.
 Unfortunately, I'm mainly dealing with only human data and don't have any
direct examples to know for sure.  I can re-process some of our EBV data
with the de novo aligner and see what can be done.

-Kevin