Alpha diversity without rarefaction

General Discussion
1

Hi Qiime2 community,

I have been going through literature regarding compositional analysis for microbiome data (or metabarcoding data in general). There is a strong opposition to the use of rarefaction for a compositional dataset.

I wonder if there are any suitable replacement specific for the calculation of alpha diversity, without the need of rarefaction.

Comparing to other types of analysis, like beta diversity, differential abundance analysis, etc. Each type of analysis are equipped with their own approach (presumbly to be the most suitable one) to tackle compositionality. However, for alpha diversity, it seems that there are no such a replacement (or perhaps I miss the literature).

I don't think I should calculate alpha diversity without any of the treatment to the raw data...Are there any recommendations or literature relevant to this issue?

Any suggestions are most welcome. Thanks

2

Hi @ivanllam,

I don't think I should calculate alpha diversity without any of the treatment to the raw data...Are there any recommendations or literature relevant to this issue?

That's exactly right.

Check out this paper/plugin from my group, and the Schloss papers that we cite in the paper (references 1 and 2).

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3

Thank you for your prompt reply. It's something exactly I am looking for!

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