Jupyter Book Tutorials¶
Warning
This site has been replaced by the new QIIME 2 “amplicon distribution” documentation, as of the 2025.4 release of QIIME 2. You can still access the content from the “old docs” here for the QIIME 2 2024.10 and earlier releases, but we recommend that you transition to the new documentation at https://amplicon-docs.qiime2.org. Content on this site is no longer updated and may be out of date.
Are you looking for:
the QIIME 2 homepage? That’s https://qiime2.org.
learning resources for microbiome marker gene (i.e., amplicon) analysis? See the QIIME 2 amplicon distribution documentation.
learning resources for microbiome metagenome analysis? See the MOSHPIT documentation.
installation instructions, plugins, books, videos, workshops, or resources? See the QIIME 2 Library.
general help? See the QIIME 2 Forum.
Old content beyond this point… 👴👵
These tutorials are powered by Jupyter Book, a Jupyter-based documentation tool developed with support from the Sloan Foundation.
The Cancer Microbiome Intervention Tutorial: A multiple interface tutorial with a corresponding video series exploring the impact of fecal microbiota transplant on cancer treatment recovery in a placebo-controlled human trial.
q2book: An Introduction to QIIME 2 and Concepts in Microbiome Bioinformatics (a work in progress)
q2-moshpit: A set of tutorials showcasing shotgun metagenomics analysis workflows