[Biopython] sff into fasta and qual -> trim

[Kiss, Csaba]

Thanks Peter for the info. I will look at the Software list.

Csaba

-----Original Message-----
From: Peter Cock [mailto:p.j.a.cock at googlemail.com] 
Sent: Tuesday, October 23, 2012 10:37 AM
To: Kiss, Csaba
Cc: Biopython Mailing List
Subject: Re: [Biopython] sff into fasta and qual -> trim

On Tue, Oct 23, 2012 at 5:22 PM, Kiss, Csaba <csaba.kiss at lanl.gov> wrote:
> Thanks, Peter.
> I understand the fastq sequence extraction. That's very neat. However, I am not sure how to do quality trimming of the sequences.
> In mothur, we tested that qwindowsize=50, qwindowaverage=22 is a very nice way to get high quality sequences out.
> I assume it works in a way that a 50 bp sliding window checks the average quality and if it's below a certain number (i.e. 22) then it rejects the sequence if it's above it keeps it.
> Is there something similar in biopython.
>
> C

Hi Csaba,

No, there isn't a 'ready to use' sliding window read cleaning tool/function in Biopython, although you could write one using Biopython is you wished, with the advantage that you can implement exactly what you need.

There are many (dozens?) of dedicated tools for this kind of thing which might be simpler or more appropriate. Have a browse here:
http://seqanswers.com/wiki/Software/list

Regards,

Peter

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