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  • memory and cpu requirement for bwa

    How much memory and CPU are required for running bwa with hg19 and a fastq file as small as the 1000 genomes ftp://ftp-trace.ncbi.nih.gov/1000gen...filt.fastq.gz?

    Thanks,

    Carol

  • #2
    You can find the memory use and running time for mapping a 1000Genomes dataset by a few popular aligners including bwa - http://www.ncbi.nlm.nih.gov/pubmed/23558742

    Comment


    • #3
      Bwa-0.5.x uses ~4GB RAM; 0.6.x+ uses ~5.1GB. On ~5-year-old machines, bwa aligns 100bp reads at ~7Gbp per CPU day; bwa-sw at ~3Gbp per day; the new component bwa-mem at ~14Gbp per CPU day (similar to bowtie2). On the latest Intel CPUs, they can be 50-100% faster.

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      • #4
        It seems that in the construction of bwa index, the step Construct SA from BWT and Occ... after
        [BWTIncConstructFromPacked] 680 iterations done. 6177547390 characters processed.
        [bwt_gen] Finished constructing BWT in 687 iterations.
        [bwa_index] 2546.24 seconds elapse.
        [bwa_index] Update BWT... 17.80 sec
        [bwa_index] Pack forward-only FASTA... 32.21 sec

        is very lengthy. What would be the acceptable amount of time for this step?

        Thanks

        Carol

        Comment

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