I would like to perform some downstream analysis on the OTU table that was generated using HMP 16s v3-v5 data. But the OTU table provided by the HMP website is very old and with QIIME 1.3 version. Since it's 2022, I'm wondering if anyone knows any publication that has reran the Qiime 2 pipeline and has the OTU table with taxa out there. So that I wouldn't need to rerun the whole pipeline just for a test downstream analysis.
Have you checked qiita? I think they have the HMP data (along with a bunch of other studies) processed and readily avaliable. There are a few differences in the tools used in Qiita than QIIME 2 (for example, I think Qiita uses SortMeRNA for clustering but QIIME 2 uses vsearch as the engine), but it should be a more "modern" table.