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  • Numerous short read aligners: But which is best?

    Hi All,

    There seems to be a bunch of competing packages out there (MIRA3, Abyss, Velvet, Bowtie etc), but I wonder if anyone can offer a comparative synopsis of the data produced by each?

    Has anyone compared assemblies between these packages, and which did they find most robust/reliable/erroneous/automated etc/?

    My interests at the moment surround transcripome assemblies, and have been using MIRA3 and Geneious (which i think uses Bowtie). The incorporation of QUAL files in MIRA3 assemblies seems like a good idea.
    Any thoughts?

    Cheers,

    J

  • #2
    See: http://assemblathon.org/

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    • #3
      Evaluation of asssembly algorithms


      BTW, MIRA3 is de novo assembly, while Bowtie is short read aligner. Not sure, but I think Geneious use their own algorithm.

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      • #4
        cheers, guys

        j

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        • #5
          Hi, Yes, Geneious uses its own algorithm inside Geneious Pro, however Geneious Server allows users on the desktops to run a range of different mappers and assemblers including SOAP2, BWA, MAQ, Bowtie and Velvet in addition to the Geneious Reference Assembler and the Geneious de novo Assembler

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