Entering edit mode
7 weeks ago
lacb ▴ 120
I would like to have an idea of the computing time required to map a big fastq with bwa-mem,
I have 2x150bp reads, 750M sequences and fastq_1 + fastq_2 = approx. 90Go,
I would like to know, in your experience, what order of magnitude of CPU time it would require ?
I know the result will vary with CPU specifications, etc, so let say with 16 CPU @ 2.5Ghz
Since this is quite specific to the actual sequence content and machine (CPU, memory, I/O) I would simply subset to a few million reads, maybe 20mio and then run and extrapolate runtime. It will be many hours for sure for 750M reads.