[EMBOSS] Trimming illumina short reads based on quality

[Peter]

On Tue, Dec 1, 2009 at 2:33 PM, michael watson (IAH-C)
<michael.watson at bbsrc.ac.uk> wrote:
>
> Hi
>
> I'm sorry if I've not been keeping up to date on what is doubtless a hot topic.
>
> Does EMBOSS allow one to trim short reads based on quality data (from a fastq file)?
>
> If not, I have read that it is planned - any idea when it will be implemented?

Not yet, but it has been proposed and I understand it is on the
EMBOSS to do list along with quality filtering (Peter Rice has
suggested the name quaffle for this):
http://lists.open-bio.org/pipermail/bioperl-l/2009-July/030493.html

I dare say suggestions for precise trimming algorithms (e.g. median
over sliding window) might be welcome.

> Otherwise, alternative suggestions are welcome!

I'm sure there are plenty of scripts out these, in Perl, Python etc.
What is your language of choice?

Peter C.