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  • vanillasky
    Member
    • Mar 2014
    • 42

    Analyzing metagenomic contigs

    I have just finished running an assembly with Metavelvet and now have the contig file. Since I am new to the assembly process I wanted to ask what programs can be used next to analyze these contigs?
  • cliffbeall
    Senior Member
    • Jan 2010
    • 144

    #2
    MG-RAST or IMG-MER, maybe?

    That's assuming you want to do annotation and you don't mind web-based tools.
    Last edited by cliffbeall; 07-02-2014, 07:21 AM. Reason: clarity

    Comment

    • vanillasky
      Member
      • Mar 2014
      • 42

      #3
      What other options are there besides the web based tools? Are the stand alone programs more advantageous?

      Comment

      • Brian Bushnell
        Super Moderator
        • Jan 2014
        • 2709

        #4
        What do you want to analyze about them? I like Quast, which is not web-based.

        Comment

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