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Mosaik Aligning with 454 Reads

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  • donniemarco
    replied
    How can I create one single dat example total.ref.dat for the entire genome. The data available are in seperate files for each chromosome.
    I want to run entire index data with mosaik for all the chromosome together.
    Thanks!!

    Leave a comment:


  • neolith
    replied
    In the case of Mosaik version 1.0.1367,
    aligned the lane of 119,263 '454 reads', in 246minutes (7.7 reads/s)
    to the entire human genome(3.0Gbp) using 8 processor cores....

    Leave a comment:


  • neolith
    started a topic Mosaik Aligning with 454 Reads

    Mosaik Aligning with 454 Reads

    How long will it take to finish the Mosaik Aligning work?

    In the manual for Mosaik1.0, MosaikAligner aligned the lane of 6,563,762 Illumina paired-end reads(36bp) in 45.9minutes (2,390 paired-end reads/s) to the entire human genome(2.9Gbp) using 8processor cores.

    And in the manual for Mosaik, Aligner setting for 454 GS-FLX : -hs 15 -mm 0.05 -act 26

    But in the case of version 0.9.891, the lane of 119,263 '454 reads'
    expected time of alignment over 50 hours.(0.6 reads/s)

    Used commands are :
    MosaikAligner -in input.dat -out aligned.dat -ia total.ref.dat -hs 15 -mm 0.05 -act 26 -m all -mhp 100 -j h.sapiens_15 -p 8

    Mosaik version : 0.9.891-linux-x64

    I will do the job with version 1.0.1367, and I want to reduce working hour...
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