[Biopython-dev] Newbler ACE file to SAM?

[Nick Loman]

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

Cheers

Nick