Hello,
I just downloaded the new version of Stacks (v2.41 from July). The pstacks module is not in the software anymore and is not documented in the manual either.
Has it been removed? If yes, has ustacks been modified in order to deal with reference-aligned reads?
Many thanks ! :)
Noé
For those who wonder, I just realised that this is the result of Stacks passing to its second version. You can see here the changes made between version one and two, it is very helpful! https://www.biorxiv.org/content/biorxiv/early/2019/04/22/615385.full.pdf
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version 2.3.6
Just for future reference, any questions on STACKS can be addressed in their google group found here. Very active community with Catchen himself being involved.