[Biopython-dev] Newbler ACE file to SAM?

[Peter]

On Wed, Aug 4, 2010 at 6:05 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.
>>
>
> 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

Or ask your Roche representatives to implement SAM/BAM output?
Mind you, as the MIRA3 author has pointed out, SAM/BAM isn't so
great for de novo assemblies. It doesn't even store the contig seq ;)

Peter