Normalization for microbiome 16s sequence analysis

[Nicholas_Bokulich]

@abalter

Regarding the rarefaction, does the waste not want not idea not apply to that metric?

Yes and no — there has been a lot of discussion on this forum about rarefaction and the arguments for/against, see this post for a nice collection of those topics:

Use of rarefacted Table

Hi @m_max, Welcome! There’s been a fair bit of discussion around rarefaction here (or maybe Im just involved in a lot of them). It’s maybe good to go look into those threads since they’ll give you a wide variety of view points. Here are a few to start that I found pretty quickly. Best, Justine

@abalter

I tried googling for QIIME2 normalization and found the normalize_table.py script and differential_abundance.py script. Both have options to use DeSeq normalization.

Those are implemented in QIIME 1, not QIIME 2

@abalter

There are also some 3rd party scripts implementing percentile normalization that have been developed:

Yes! q2-perc-norm is a QIIME 2 plugin! You can see the QIIME 2 plugin library to see these and other plugins (some of which use alternative normalization techniques, including @mortonjt's methods)

@abalter

I’m not fully versed, but it seems to me that the more biological/clinical microbiome literature is well behind the improved methods being developed.

Microbiome data normalization and differential abundance methods are very active areas of research, and of debate.

@abalter

This is a hot area I hope to explore!

It is hot! Best of luck and any new methods you use/implement please consider adding to QIIME 2!