[Biopython-dev] Newbler ACE file to SAM?

Kevin Jacobs <jacobs@bioinformed.com> bioinformed at gmail.com
Wed Aug 4 17:11:28 UTC 2010

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.


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