Normalization of biom or qza file

Hi all.

(Thank you for developer that I can analyze microbial composition.)

I’d like to normalize my biom file (or table.qza imported from biom file to QIIME2).
When I use QIIME1, I usually typed single_rarefaction.py to normalize for the lowest sample depth without additional file.
But in QIIME2, I can’t find normalizing protocol the same as QIIME1.
Actually, there is “qiime diversity core-metrics-phylogenetic” that gives me normalized .qza file. But I have to prepare phylogeny tree file…

I just want to normalize my “OTU table” without any other files.

Some one help me, please.

Best,
Denny

1 Like

Good morning Denny,

Welcome to the forums! :qiime2:

:point_right: https://docs.qiime2.org/2019.10/plugins/available/feature-table/rarefy/

Let us know if you have any questions!


The ‘scripts’ in Qiime 1 have been replaced in Qiime 2 by ‘plugins’. You can see all the current plugins here, and control+F to Find features you need:
https://docs.qiime2.org/2019.10/plugins/available/

Colin

3 Likes