How many threads to use for SEPP?

Hi everyone,

I am new to the world of bioinformatics and am looking for some general advice on how many threads to run various commands on (e.g. currently using
“qiime fragment-insertion sepp” command). I am working on a Mac with 12 cores, ubuntu installed, 24 GB of memory, and an Intel Xeon processor. I thought that there were only two threads per core, but when I check out the activity monitor, I see many more than 24 running. I haven’t been able to find a good explanation of threads per core online! Could anyone please explain threads per core or offer a link to a resource I might checkout? Also advice on how many threads I should run fragment-insertion sepp on for the best performance would be very much appreciated! Thanks in advance! :~)


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Hi @ccwinfrey

Check out this link:

As many as you can!


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