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  • Mapping benchmarks of the GMS

    Hi,

    As I promised in another thread here some first controlled benchmarks from the Genomatix Mapping Station ( GMS):
    • Random pick of 1Mio reads (32bps) across the human genome (NCBI build 36)

    • Generate 1bps insertions and 1bps deletions in 1% of the reads
    • Generate 1 bps substitutions in 10% of the reads


    Mapping time: 375 seconds

    Correctly identified reads: 921.799 (92 %)
    Found perfect alignment for read with indel: 2.653 (0.2%)
    Ignored because ambiguous: 43.057 (4%)

    =====================================
    Real life data:

    Illumina: ChipSeq STAT1 human
    Total: 5.069.935 reads
    Length of reads: 36

    Time: 1.524 sec (about 5 min per 1.000.000 reads)

    Result:
    4.150.890 unique best hits (81 %)
    3.151.593 with alignment score > 0.9
    207.636 of the unique hits with alignment score > 0.9 have at least on insertion or deletion in the alignment
    560.920 reads with multiple best hits

    ====================================
    Real life data:

    Helicos DGE human tissue

    Total: 4.397.276 reads
    Length of reads: 5bps to 140bps

    Time: 527 sec

    Result:
    1.662.837 sequences were ignored (too small) (37 %)
    2.011.375 unique best hits (45 %)
    777.434 with alignment score > 0.9
    665.631 of the unique hits with alignment score > 0.9 have at least on insertion or deletion in the alignment
    723.064 reads with multiple best hits

  • #2
    This looks good.

    What Hardware conditions e.g. RAM, CPU clock speed, etc are these benchmarks running on?

    Comment


    • #3
      How does it compare to the Eland alignments (e.g. # aligned sequences etc) for STAT1? Was the DGE alignments done with or without splice junctions?

      Comment


      • #4
        Hi,

        no fancy hardware, just an opteron processor, 2GHz
        but 64GB of main memory!

        ->Chipper: I am travelling in the US this week. I´ll try to give you some answers later, or ask a colleague to jump in.

        Klaus

        Comment


        • #5
          Eland was designed to avoid having 64Gb of memory. It should do about 4000 reads per second per CPU on a modern CPU so ~250 seconds.

          Comment

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