454 sequence data filtering

[amb1networks]

Hi all!

I'm working on a pipeline that deals with 454 data analysis. First step is to filter the 454 sequences, thus removing primers, low quality sequences and sorting them based on sample (MID tags used for identification.) From RDP site I came to know that GS-FLX software does such filtering but seems it's proprietary. Do you know any such command line based standalone software for filtering?

Thanks,

Anand

[nickloman]

I believe there are numerous pipelines that can do this, but one option you might consider is QIIME (qiime.sourceforge.net).

Or you could write your own scripts using BioPython which supports SFF format.

[flxlex]

Have you tried google? Here are some hits supplemented wih two I knew of before:

CANGS http://www.biomedcentral.com/1756-0500/3/3
mothur http://www.mothur.org/wiki/Trim.seqs
fastx http://hannonlab.cshl.edu/fastx_toolkit/
obitools http://www.grenoble.prabi.fr/trac/OB...ytouseobitools

[Palecomic]

I would second the qiime recommendation, it's a nice pipeline with active development and there are lots of ways of running it.