How do I multithread PoPoolation?
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2.5 years ago
James Reeve ▴ 130

I'm trying to call nucleotide diversity for a pool-seq dataset using PoPoolation's Variance-sliding.pl. However it's taken over a day to run one chromosome. I want to speed this up,

Does anyone know how to multi-thred PoPoolation, or other tips that could get it running quicker?

My Code:

perl popoolation_1.2.2/Variance-sliding.pl --input in.mpileup --output out.varslid.pi \
--measure pi --min-count 2 --min-qual 20 --min-coverage 50 --pool-size 100 \
--window-size 1000 --step-size 1000
PoPoolation optimization • 569 views
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I don't think popoolation natively supports multi-threading. You will need to break the jobs up into pieces and brute force parallelize on your own (see: popoolation parallelization problem )

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