Utility of rarefy function and rarefaction?

[Nicholas_Bokulich]

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:

Rarefraction not advantageous to detect differences in beta-diversity

Hi @Alfred.Burian, Thanks for bringing this up! Without wading too far into this debate, I will point out that rarefying is not always inadmissible, particularly for unweighted UniFrac and other beta diversity methods based on presence/absence of features. This is actually also shown in Fig 4 of the article that you posted, though for other distance methods other normalization strategies perform better. Second, what you describe is the qiime diversity core-metrics-phylogenetic method, which r…

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.