QIIME 1 Script Equivalent in QIIME 2 - summarize_taxa.py, alpha_diversity.py, beta_diversity.py

[jconoranderson (Conor Anderson)]

I'm carrying out diversity and relative abundance analysis on a 16S sequenced dataset that I have run through the dada2 pipeline to create the OTU table - DADA2 Pipeline Tutorial (1.16)

and converted it to the hdf5 .biom format - Converting between file formats — biom-format.org

The problem I am running it is that team I am working with are still operating on qiime 1 and have not upgraded, and am having trouble finding tutorials for the specific analysis I am doing. As a work around was able to run qiime 1 on a virtual machine but that is not a good long term strategy.

Can anybody point me in the direction of tutorials to run the equivalent of the summarize_taxa.py, alpha_diversity.py, and beta_diversity.py scripts found here - QIIME Scripts — Homepage in qiime 2?

[colinbrislawn (Colin J Brislawn)]

Hello Conor,

@jconoranderson

scripts found here

The scripts of Qiime1 have been replaced by Qiime2 "plugins", and you can see all the core plugins here.

Most names are the same, but some are a little different:

• summarize_taxa.py -> collapse: Collapse features by their taxonomy at the specified level — QIIME 2 2022.8.3 documentation
• alpha_diversity.py and beta_diversity.py -> https://docs.qiime2.org/2022.8/plugins/available/diversity/

We also have community-made plugins that extend Qiime2 in useful ways.

And, of course, let us know if you have any questions!

Welcome to Qiime2!

P.S. If you haven't found these already, check out the comprehensive tutorials for examples of how to use these plugins to process data.