On Tue, Dec 1, 2009 at 2:33 PM, michael watson (IAH-C) <[email protected]> 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. _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
