[Biopython-dev] Newbler ACE file to SAM?

[Peter]

On Wed, Aug 4, 2010 at 5:32 PM, Nick Loman <n.j.loman at bham.ac.uk> wrote:
>
> Kevin Jacobs <jacobs at bioinformed.com> wrote:
>>
>> I may have mislead you-- I use the 454PairAlign.txt and SFF files together
>> to generate SAM/BAM files with full untrimmed read data and quality values.
>>  My recollection was that the Newbler ACE files contained only the consensus
>> sequence and not the individuals reads, which is why I didn't go down that
>> road.  I routinely use "-noace" so I'm quickly realigning a small dataset to
>> generate an example ACE file to verify this.  If I am incorrect and
>> alignment information is indeed available from the ACE files, I'll happily
>> add support for them to my converter.
>
> Hi Kevin
>
> I'm pretty sure the ACE files contain the individual reads (or at the least,
> the trimmed, aligned portions of them) because this is the file one uses in
> Consed/Tablet to view an assembly.

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.

>
> We may of course be talking at cross-purposes!
>

Maybe :)

Peter