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  • Powerful PC for MOSAIK aligner?

    For mapping 454 reads against human genome with MOSAIK, which configuration would you recommend?
    PC with
    a) two quad core 2.26GHz processors and 24GB RAM or
    b) two quad core 2.40GHz processors and 12GB RAM

    in other words, whats more important: the processor or RAM capacity?

  • #2
    My jump database was about 20 GB in size. Having that all in memory is much faster than swapping to disk. So I'd go for the large memory but it really depends on the size of the jump database you will use.

    Comment


    • #3
      Originally posted by neni View Post
      For mapping 454 reads against human genome with MOSAIK, which configuration would you recommend?
      PC with
      a) two quad core 2.26GHz processors and 24GB RAM or
      b) two quad core 2.40GHz processors and 12GB RAM

      in other words, whats more important: the processor or RAM capacity?
      This may help you:

      http://seqanswers.com/forums/showthread.php?t=2566
      -drd

      Comment


      • #4
        Hello everybody,
        I'm struggling with the same problem.
        I'm on the way to buy a desktop/workstation.
        My project is the following- eukaryote-plant
        -454 EST assembly 1,5 M reads from 3 different samples (for SNP mining)
        Looking to use MIRA, the extimated memory usage is 8 Gb. OK
        -Solexa reads (always from cDNA) mapping to reference sequence (generated
        by 454) ; aprox. 30 M reads to map (always for SNP mining on other
        samples).For this one I'm looking to use MOSAIK (MIRA gave me an exitation
        of memory around 30 Gb).

        The question is the following:
        Does a desktop/workstation with a quad-core (intel i7 860) with 12 Gb can handle this kind of Solexa mapping, or, any scripts will run out of memory??
        I'm also considering to install 24 Gb instead of 12 Gb but I cannot understand if this might be crucial or just wasted money (because there is no way to run a Solexa mapping without a powerful cluster).
        I mean, I don't care if the assembly will take one or two days; but I just wanna make sure it will be accomplished without crashing. In other word, having a cluster with 256 Gb of RAM, is just a matter of run time or it is the pivotal point to avoid the assembler to crash?

        Can anyone give me some highlight on what I should expect from such a machine I'm planning to buy.

        Thanks, I will appriciate.

        Davide

        Comment


        • #5
          Originally posted by Gianza View Post
          Hello everybody,
          I'm struggling with the same problem.
          I'm on the way to buy a desktop/workstation.
          My project is the following- eukaryote-plant
          -454 EST assembly 1,5 M reads from 3 different samples (for SNP mining)
          Looking to use MIRA, the extimated memory usage is 8 Gb. OK
          -Solexa reads (always from cDNA) mapping to reference sequence (generated
          by 454) ; aprox. 30 M reads to map (always for SNP mining on other
          samples).For this one I'm looking to use MOSAIK (MIRA gave me an exitation
          of memory around 30 Gb).

          The question is the following:
          Does a desktop/workstation with a quad-core (intel i7 860) with 12 Gb can handle this kind of Solexa mapping, or, any scripts will run out of memory??
          I'm also considering to install 24 Gb instead of 12 Gb but I cannot understand if this might be crucial or just wasted money (because there is no way to run a Solexa mapping without a powerful cluster).
          I mean, I don't care if the assembly will take one or two days; but I just wanna make sure it will be accomplished without crashing. In other word, having a cluster with 256 Gb of RAM, is just a matter of run time or it is the pivotal point to avoid the assembler to crash?

          Can anyone give me some highlight on what I should expect from such a machine I'm planning to buy.

          Thanks, I will appriciate.

          Davide
          You can also buy two 15K RPM SAS drives or two WD 10K SATA drives to form RAID0 for the swap memory. You can try this before you spend big money on the RAM.

          Comment

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