[Biopython-dev] Newbler ACE file to SAM?

[Kevin Jacobs <jacobs@bioinformed.com>]

On Wed, Aug 4, 2010 at 1:05 PM, Nick Loman <n.j.loman at bham.ac.uk> wrote:

> Peter wrote:
>
>> Yes, they do. But ACE files lack the quality scores for the reads (they
>> just have quality scores for the consensus) which are required for SAM
>> or BAM. You'd have to insert dummy values or get them from another
>> file - Kevin says he takes them from the SFF file.
>>
>>
>
> Right, that makes sense. In which case it should be possible to convert ACE
> (when accompanied by the SFF files), as an alternative to using
> 454PairAlign.txt as the input file. Certainly the ACE file contains the
> unique 454 read identifiers that would make it possible to pull read
> qualities from the SFF, although you would have to watch out for the Newbler
> partial read alignments (READ_ID.NtoN style)
>
>
In that case, I'm happy to add support for those ACE files.  My code already
handles the NtoN trimming from the 454PairAlign files.  If you'd like to
send me (off list) a small example ACE file, I can likely have it working
very quickly.

-Kevin