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  • AnthonyB
    Junior Member
    • Sep 2008
    • 8
    #1

    SOAPdenovo

    Has anyone tried the new SOAPdenovo program for assembling short reads and compared it to velvet etc? Their website claims that it can assemble human-sized genomes (eg panda) without crazy-high RAM (~150Gb) requirements.
    Tags: None
    • GerryB
      Member
      • May 2009
      • 12
      #2
      Actually their website says the opposite.

      Originally posted by SOAP site
      SOAPdenovo aims for large plant and animal genomes, although it also works well on bacteria and fungi genomes. It runs on 64-bit Linux system with a minimum of 5G physical memory. For big genomes like human, about 150 GB memory would be required.

        Comment

        • AnthonyB
          Junior Member
          • Sep 2008
          • 8
          #3
          I guess I should have been clearer in my post to say that the 150GB RAM requirement of SOAPdenovo for a human sized genome seems to be much lower than estimates I've seen for other short read de novo programs (>500GB RAM).

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