Normalization for microbiome 16s sequence analysis

[Nicholas_Bokulich]

@abalter

would you say that doing the standard routine (alpha, beta, igaseq, regression, etc.) on some sort of normalized data rather than raw data would be an improvement?

Definitely some sort of normalization is required for most analyses, but the same sort of normalization may or may not be appropriate for all methods.

In QIIME 2 we handle this by having each method (mostly) perform the normalization that is required. So a couple examples:

1. alpha/beta diversity methods have their own normalization (rarefaction in the core-metrics pipelines; see q2-breakaway for a more sophisticated method for attempting to estimate the true alpha diversity if rarefaction is upsetting)
2. differential abundance methods have their own normalization procedures on-board (e.g., see ANCOM or @mortonjt's methods)

It would be awesome to see other normalization methods implemented in QIIME 2 and we have some open issues — if you are interested in getting involved please let us know!