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  • Classify Bacterial and Archaeal fragments from 454-Metagenome

    Hello all,
    I have just started working with 454 metagenome datasets and was wondering if there is any tool that can classify reads from 454 into bacterial or archaeal sequences?

    I have come across many tools that do something similar only for 16s rRNA.

    Using a training dataset and word based classifier, can one divide the metagenome dataset into bacterial and archaeal sequences?

    Thank you for your time!!

  • #2
    MGRast

    Have you looked into MGRAST? It is a free webserver with lots of functionality.

    Comment


    • #3
      Thank you for you suggestion.

      Yes, I have. I would really like something that has a lot of standalone capacity instead of a webserver....

      Comment


      • #4
        MetaPhlAn (http://huttenhower.sph.harvard.edu/metaphlan/)

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        • #5
          Thank you jimmybee! MetaPhlAn looks good.

          Any more recommendations?

          Once again, thank you for all your solutions.

          Comment

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