Utility of rarefy function and rarefaction?

I see there are already some discussions on this topic in the forum, but that the rarefy function still exists. Copy/pasting from original Github comment:

" I'm unsure if this may be too bold of a comment, but may rarefaction now be obsolete? I've been reading a good deal about the artifacts that can arise with rarefying these past few months and perhaps this is a function worth getting rid of as part of the surmounting statistical evidence?

ie Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible "

Hi @sabahzero,
Great question! I think it is too early to call rarefaction obsolete, though it is certainly on its way out the door. Your question is a replicate of some previous posts — see this response:

So it is still quite useful to expose functionality that a very large number of users still rely on.

Similarly, QIIME 2 has several methods for OTU clustering, which is still very popular (and useful for some applications), even though denoising methods are theoretically much better.

Thank you for the quick and thorough reply, @Nicholas_Bokulich! These are helpful to read. I skimmed through some of them, but good to refresh.

Agree it’s popular, but is it correct statistically? That’s where I’m a bit uncertain and agree it may be on its way out.