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  • mads b
    replied
    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!

    Leave a comment:


  • entropy
    replied
    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!

    Leave a comment:


  • flxlex
    replied
    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.

    Leave a comment:


  • 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

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