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  • 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?

  • #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

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

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

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