[Biopython-dev] Newbler ACE file to SAM?

[Kevin Jacobs <jacobs@bioinformed.com>]

On Wed, Aug 4, 2010 at 12:18 PM, Nick Loman <n.j.loman at bham.ac.uk> wrote:

> 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.
>
>
Hi Nick,

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.

-Kevin