[Biopython] Adaptor trimmer and dimers

[natassa]

Thanks Peter, 
I ve gone through these posts already, so my question was whether a global alignment script exists-Brad Chapman's script does a local alignment. Also, I would be mostly interested in discarding adapter-dimer reads and I do not find any adaptation on his code to detect those, unless I am wrong.. I would also like to discard their pairs, as I am inputting those to velvet assembler which takes into account the pair-read information for scaffolding. 
I can try to  write up something integrating the above features, I was just wondering if there is anything out there already and whether people find this a sensible approach.
Kind regards, 
Anastasia 
--- On Thu, 10/15/09, Peter <biopython at maubp.freeserve.co.uk> wrote:

From: Peter <biopython at maubp.freeserve.co.uk>
Subject: Re: [Biopython] Adaptor trimmer and dimers
To: "natassa" <natassa_g_2000 at yahoo.com>
Cc: biopython at lists.open-bio.org
Date: Thursday, October 15, 2009, 12:20 PM

On Thu, Oct 15, 2009 at 5:00 PM, natassa <natassa_g_2000 at yahoo.com> wrote:
> Hallo Biopythoners,
> I followed a recent thread conversation about adaptor trimming,
> which I intend to do on Illumina runs, and I am not sure I know
> where exactly in github I could find Brad Chapman's code for
> trimming AFTER modifications that he has done based on the
> thread conversation. ...

I guess you mean Brad's August Blog Post:
http://bcbio.wordpress.com/2009/08/09/trimming-adaptors-from-short-read-sequences/
and the following mailing list thread which included some tips on
speeding up the Biopython side of things:
http://lists.open-bio.org/pipermail/biopython/2009-August/005417.html

For anyone else interested, there are some simple examples in the
tutorial (using SeqRecord slicing - elegant and simple, but a bit slow):
http://biopython.org/DIST/docs/tutorial/Tutorial.html#sec:FASTQ-slicing-off-primer
http://biopython.org/DIST/docs/tutorial/Tutorial.html#sec:FASTQ-slicing-off-adaptor

And I did a blog post about low level FASTQ handling for speed
at the cost of flexibility and simplicity (using some of the same
ideas from the August mailing list discussion):
http://news.open-bio.org/news/2009/09/biopython-fast-fastq/

Peter