[Biopython-dev] Newbler ACE file to SAM?

[Kevin Jacobs <jacobs@bioinformed.com>]

On Wed, Aug 4, 2010 at 10:48 AM, Nick Loman <n.j.loman at bham.ac.uk> wrote:

> Hi biopython-developers,
>
> Has anyone written any code to convert ACE files (Newbler ACE, in
> particular) to SAM format?
>
>
Hi Nick,

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.).

I also know that the Roche/454 folks are adding SAM/BAM support to a future
version of Newbler, but I wouldn't expect to see that for at least a few
more months.

-Kevin