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  • Meta-Velvet

    Hi,

    I have been using Meta-Velvet for assembling my nucleotide sequences. However, i have run into some issues as the size of my data is very large. Can anyone tell me if i can break my file up and then assemble it and still get the same results?

  • #2
    ABYSS assembler can be used for huge data assembly.

    Comment


    • #3
      Can you
      a) cluster data first ? Try CD-hit ?
      b) remove contaminants first ?
      c) get time on a large mem server ?
      d) look into the cloud ?

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      • #4
        Hi Colindaven, it is a good idea. We really did several tests using CD-HIT before. We got better assembly results than original dataset. did you also use CD-HIT for assembly test?

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        • #5
          That's interesting. Nope, haven't used CD-Hit for metagenomic data before, but may have to do so soon depending on how much of our forthcoming metagenomics data is mappable.

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