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FelixKrueger / Bismark

A tool to map bisulfite converted sequence reads and determine cytosine methylation states
http://felixkrueger.github.io/Bismark/
GNU General Public License v3.0
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suggestion for -p #608

Closed AlisaGU closed 1 year ago

AlisaGU commented 1 year ago

Hi, I noticed that the suggested value for -p parameter is 4. Maybe it depends on the reference genome size. My reference genome is 47G. After test with -p 4 -p 10 -p 20, running time for 1000,000 read pairs is 144min, 75min and 36 min. It's clear that -p 4 is no more the best parallel value.

FelixKrueger commented 1 year ago

Thanks for your suggestion, I might just change the recommendation to 'needs to be determined empirically' in the future. Cheers, Felix