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

    Leave a comment:


  • flxlex
    replied
    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

    Leave a comment:


  • nickloman
    replied
    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.

    Leave a comment:


  • amb1networks
    started a topic 454 sequence data filtering

    454 sequence data filtering

    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

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