[Biopython-dev] Newbler ACE file to SAM?

[Nick Loman]

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.
>   
Hi Peter

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)

Cheers

Nick