Ways to speed up pilon - Githubissues

broadinstitute / pilon

Pilon is an automated genome assembly improvement and variant detection tool

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Ways to speed up pilon #134

Open kattweigh opened 3 years ago

kattweigh commented 3 years ago

Hi there!

I am using pilon to polish contigs produced in a hybrid assembly using opera and pilon is running at a really slow rate - about 102 contigs per hour. I have allocated 48 CPUs and 1.5Tb mem to the job and specified 200Gb to each process.

Are there any ways to improve the speed?

Thank you!

Kat

alimayy commented 2 years ago

@kattweigh changing the '--fix' parameter value from 'all' to 'bases' should help. The latter doesn't fix for local assembly errors which saves time