Nick Stoler

Oops, I missed that section of the README! Thanks for pointing this out.

Re-opening with the addition of `--cons-thres` to the list.

Thanks for the report! Could you check which version of Du Novo you're running? A quick `correct.py --version` should tell you.

Alternatively, use the MD tag to only filter out variants that occur in that region, not the sequence.

Thanks for reporting, @thi-trinh. I'm re-opening this to track the issue when installing via toolshed, which is still supported in the code for now (probably deprecated in the future).

One solution would be to replace the NVC with another variant caller, like Freebayes or Detect.

Update: 88b2e02 didn't fix this, but it reduced memory usage so that it's now very similar to MAFFT. Suggests it could be the same underlying issue, independent of the particular...

Idea: Maybe set `maxtasksperchild` on `multiprocessing.Pool` and see if replacing workers periodically helps.