fungal ITS analysis with QIIME2: current recommended workflow?

Thank you for continuing this discussion. I'm glad folks are thinking about this deeply as we have been since 2019.

I didn't make the 97% databases for a while, as I don't think these should be used for taxonomy.
But folks asked for them :person_shrugging: :violin:

Let's add this: much of amplicon analysis is based on bacteria, Illumina, and the 16S gene.
Like, four tutorials on this page use the 16S V4 region.
Assumptions lead to mistakes.

Variable-length genes break all sorts of assumptions. @Robert_Edgar wrote that up too:
https://drive5.com/usearch/manual/global_trimming_and_abundance.html

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