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  • Velvet de novo assembly to amosvalidate

    Has anyone successfully put a Velvet de novo assembly (*.afg) file through amosvalidate? Specifically, GS FLX data without a reference genome?
    I can't seem to generate a valid amos-bank (error: No library account found in bank). I hope I'm not missing the obvious.

    Thanks for any pointers.
    Canuck

  • #2
    Velvet de novo assembly to amosvalidate

    Also tried with no luck using .afg file produced from Solexa paired-end run. I was able to generate the bank and view it with Hawkeye, albeit painfully slowly, but ran into errors when running amosvalidate. Interested to know if you got it to work.

    D

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    • #3
      Velvet de novo assembly to amosvalidate

      No. I got only as far as you. Amosvalidate also failed for me. Sorry I haven't looked at this for quite a while and haven't tried anything further.

      On another topic, do you know of any way to visually compare two assemblies simultaneously?

      Thanks,
      Canuck
      Canuck

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      • #4
        How big are those assemblies / expected genomes?
        --
        bioinfosm

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        • #5
          From my recollection, the genome size was 5Mbp (bacterial genome).
          Canuck

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          • #6
            I have tried to run amosvalidate on a bank made from a velvet.afg file as well, no luck yet.

            Does anyone know how to perform the amosvalidate on a .bnk file derived from velvet_.afg file?

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