@Nicholas_Bokulich thanks! Regarding the rarefaction, does the waste not want not idea not apply to that metric?
I tried googling for QIIME2 normalization and found the normalize_table.py script and differential_abundance.py script. Both have options to use DeSeq normalization. There are also some 3rd party scripts implementing percentile normalization that have been developed:
I couldn’t find one that does ANCOM.
Is ANCOM normalization implemented in QIIME2?
I’m not fully versed, but it seems to me that the more biological/clinical microbiome literature is well behind the improved methods being developed.
I did a small amount of Google sleuthing just now and found that there are quite a few papers developing percentile methods or other ways to better normalize compositional data.
This is a hot area I hope to explore!