[Biopython-dev] Newbler ACE file to SAM?

[Nick Loman]

Kevin Jacobs <jacobs at bioinformed.com> wrote:
> I have a converter that uses the 454PairAlign.txt format to convert to 
> SAM/BAM as part of the GLU package 
> (http://code.google.com/p/glu-genetics). Their ACE files are a bit 
> problematic, though I do not remember the exact reasons offhand.  I'll 
> revisit the issue, since the alignment records are only half of the 
> conversion, since most folks also want untrimmed reads and quality scores.
>
> Aside from the input format, the only difficulty with my converter are 
> the dozen or so annoying pre-requisite packages to install to use it 
> (Python, HDF5, pytables, numpy, scipy, ply, biopython, etc. etc.).
Hi Kevin

Thanks for your email. I was aware of glu-genetics and will give it a 
whirl. The main reason I wanted an ACE file converter is that I 
mistakenly thought that the de novo component of Newbler won't produce 
the 454PairAlign.txt file, but reading the manual I see that file can be 
produced by supplying the -p (or -pt, for tab delimited output) option. 
But as you say, getting quality scores would be useful so I would be 
interested to know any progress you might make with an ACE converter.

Cheers

Nick