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  • de novo assembler for 50 million reads on a desktop machine

    Does anyone know if such a software exists?
    Soft genetics nextgene can do 10 million reads on a 8Gb Ram desktop are there others out there? commercial or open source
    http://kevin-gattaca.blogspot.com/

  • #2
    The best and easiest I ve found so far is Velvet.

    50m reads on an 8Gb machine is probably pushing it though.

    Otherwise, Edena is ok, and I had issues installing Abyss on linux.

    col

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    • #3
      Hi Kevin,

      We are about to release a beta-version of our new de novo assembler which is able to assemble large amounts of data on modest hardware. Data can be combined from various platforms and protocols.
      You can read more about the specs here:
      Welcome to QIAGEN Digital Insights LabCorp uses QCI and HGMD to improve identification and interpretation of genetic variants within inhereited diseases.Read...



      Although the benchmarks are made with 30+ Gb RAM it runs nicely on 8 Gb machines as well for the data amount you mentioned.

      Cheers

      Roald Forsberg

      **************Disclaimer: I work for CLC bio***************

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