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broadinstitute / pilon

Pilon is an automated genome assembly improvement and variant detection tool
GNU General Public License v2.0
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number of threads #25

Closed JahnDavik closed 7 years ago

JahnDavik commented 7 years ago

Hi, I am running pilon on a canu assembly with ~4k contigs with an average length of ~100kb. In the manual/tutorial I have it is stated that the '--threads' command line option is experimental. Is there any reason not to use more threads than the default (=1)?

jahn

w1bw commented 7 years ago

You should get some speedup, but not orders of magnitude, as the multithreading is pretty coarse-grained (it processes the input fasta elements in parallel, at the expense of memory and more garbage collecting). In my tests on a smaller genome, I got 3-4x using --threads 8.