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  • a GB genome with SE PE data

    1gb + genome, 100gb + sequence data (solexa)

    What are people's thoughts for de novo assembly? RAM being the limiting issue, and of course the speed and accuracy if less of RAM is used

    and there are a lot of deNovo assembly tools which I was unfortunately not able to follow .. so your feedback is very welcome.

    thanks
    --
    bioinfosm

  • #2
    Originally posted by bioinfosm View Post
    1gb + genome, 100gb + sequence data (solexa)

    What are people's thoughts for de novo assembly? RAM being the limiting issue, and of course the speed and accuracy if less of RAM is used

    and there are a lot of deNovo assembly tools which I was unfortunately not able to follow .. so your feedback is very welcome.

    thanks
    The best de novo assembly tool is velvet but also euler-sr gives good performances. I think is quite hard assembly a so large amount of data, I think you are oblige to divide it into several sets and assembly independently and then try to combine the results together

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    • #3
      I'm in the process of doing just that (1GB genome done with Illumina data), I'll post my results.
      I'll first have a go with SOAPdenovo, see where that leads me.

      Comment


      • #4
        Have you considered using abyss?

        Widespread adoption of massively parallel deoxyribonucleic acid (DNA) sequencing instruments has prompted the recent development of de novo short read assembly algorithms. A common shortcoming of the available tools is their inability to efficiently assemble vast amounts of data generated from large …

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