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Old 11-04-2011, 05:26 PM   #4
adaptivegenome
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We use similar machines and we find BWA scales perfectly, in that 48 cores enable mapping nearly 48 times faster than 1 core. We load data directly to the computer's internal RAID because otherwise the I/O is unbearably slow. We regularly map human genomes and memory has not been a bottleneck for us. We don't divide our SAM files. Are you making SAM files and then converting to BAM? If so, that can be sped up by directly streaming the mapper to samtools for conversion to BAM...

Last edited by adaptivegenome; 11-04-2011 at 05:26 PM. Reason: typos
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