[Biopython-dev] [Biopython] Adaptor trimmer and dimers

[Jose Blanca]

We also have some code to do that using exonerate. Take a look at the function 
create_vector_striper_by_alignment in 
http://bioinf.comav.upv.es/svn/biolib/biolib/src/biolib/seq_cleaner.py

Jose Blanca

On Thursday 15 October 2009 18:20:47 Peter wrote:
> 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-seq
>uences/ 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
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-- 
Jose M. Blanca Postigo
Instituto Universitario de Conservacion y
Mejora de la Agrodiversidad Valenciana (COMAV)
Universidad Politecnica de Valencia (UPV)
Edificio CPI (Ciudad Politecnica de la Innovacion), 8E
46022 Valencia (SPAIN)
Tlf.:+34-96-3877000 (ext 88473)