Parallelize truncate_reverse_primer?

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Alison Cleary

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Jan 13, 2016, 9:25:36 PM1/13/16
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Hi,

I'm wondering if there's a way to run truncate_reverse_primer in parallel on multiple cores. I'm processing paired end illumina reads, and I'd like to remove the primers and any following sequence. I'm running on a multi-core computing center, but truncate_reverse_primer seems to only be running on one core at a time and is taking forever to get through a couple of MiSeq runs (at it's current rate it may take 8-10 hrs). Any way to run this in parallel to cut down on run time?

Thanks!
Alison

Colin Brislawn

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Jan 14, 2016, 2:27:27 PM1/14/16
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No. :-(


(If you are a Linux wizard, you could chop up the files from each MiSeq run, use the script on each part, and join the results back together. But this is beyond what qiime can do.)

Good luck!
Colin Brislawn
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