[Biopython] How to optimize ACE file alignment (from newbler)

[Peter Cock]

On Tue, May 3, 2011 at 1:22 PM, Martin Mokrejs
<mmokrejs at fold.natur.cuni.cz> wrote:
> Hi,
>  I would like to ask you how can I optimize the ACE alignment with files
> produced by newbler. I see only the high-quality region is aligned while
> the rest is not. I typically ask newbler to place into the ace files untrimmed
> reads so the low-quality sequence is present, you can see it could have been
> included in the alignment and contribute the consensus quite well.
>  I found a new feature of consed-20 being able to re-align the reads
> but that seemed to be too slow for me and had to kill re-processing of one
> contig.
>  Is there a way to direct some program that I want to re-align just some
> columns since some position? That should first align to the consensus already
> defined and afterwards continue with de novo alignment as long as it is possible.
>  Alternatively, how do you edit ACE alignments (I mean manually adjust gaps,
> move columns back and forth, re-order rows) and do you re-calculate the
> consensus?
>  This is some sort of a follow-up to "Newbler ACE file to SAM?"
> posted to biopython-developers list at http://web.archiveorange.com/archive/v/5dAwXxUKZDTmQdM80MqQ
> ;)
> Martin

Hi Martin,

Biopython only has an ACE parser, with no support for writing ACE files.
So, even if you did manipulate the parsed ACE file in Biopython, you'd
have to write your own output code (or use a simpler file format).

Regarding assembly editors, have you looked at Gap4 or Gap5?

This might be a good question to ask on the http://seqanswers.com
forum.

Peter