it is not necessary to do both β if you've read otherwise in our documentation, please tell us where so we can get that fixed ![]()
Absolutely.
That normalization is not adequate for some analyses (e.g., alpha diversity comparisons require normalization for uneven sequencing depth between samples β currently we recommend rarefying to correct for that)
Any analysis in QIIME 2 (at least for "core" plugins) that requires normalization has that normalization built in β e.g., rarefying is performed automatically for alpha and beta diversity analyses. Rarefied tables should not be used for downstream analyses, e.g., that involve converting to relative abundance.
Did you have a particular step in mind?