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  • Computer hardare recommendations for assembly and annotation?

    Hi all.

    Just wondering what would be a reasonable workstation for assembling a 5.5bp bacterial genome? I'm leaning towards 454 rather than Illumina or SOLiD, but I assume the later two would need a lot more power due to the smaller reads... Any suggestions?

    Thanks

  • #2
    1 cpu, 4 GB memory would probably do the trick. Having more cpus will speed it up, though. This is assembly only, I don't know about annotation.

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    • #3
      Originally posted by flxlex View Post
      1 cpu, 4 GB memory would probably do the trick. Having more cpus will speed it up, though. This is assembly only, I don't know about annotation.
      Ok. Good to know. Thanks!

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      • #4
        We have been using a std 32bit desktop with 4gb RAM and open source software for bacterial genomes and Illumina reads. It´s doable but some steps are 4-6 hours.

        My current solution is a 64bit 2X XEON5500 quadrocore processors with 32 GB RAM. Commercial software (Genomic Workbench Clcbio). This is running smoothly and a de novo assembly of a bacterial genome is done in 10-15 min. My experience is: The faster the computer, the more likely you are to play around with parameters!

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