Alpha Rarefaction

[Aditya Bandla]

Hi

Is the alpha rarefaction analysis carried out using alpha_rarefaction.py valid for workflows where OTUs are picked de novo and when singletons are discarded (like in the UPARSE pipeline)?

Thanks in advance

Best,

Aditya

[jonsan]

Hi Aditya, 

Singleton removal is quite a common procedure in the literature, but it's a complex and difficult topic. See this paper for an in-depth technical analysis on the consequences of different parameter choices in these sorts of analyses. Singleton removal has a large effect on alpha diversity estimates -- but whether the estimates are more accurate before or after singleton removal depends a lot on your assumptions about what those singletons represent.

In general, I think our ability to make comparative assessments of diversity within a study using these methods is still much greater than our ability to make precise absolute statements about the starting sample.

-jon