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?
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.