This is the “old” QIIME 2 user documentation¶
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This site has been replaced by the new QIIME 2 “amplicon distribution” documentation, as of the 2025.4 release of QIIME 2.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 Content on this site is no longer updated and may be out of date.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… 👴👵
Table of contents¶
- Getting started
- What is QIIME 2?
- Core concepts
- Installing QIIME 2
- Jupyter Book Tutorials
- Tutorials
- Overview of QIIME 2 Plugin Workflows
- QIIME 2 for Experienced Microbiome Researchers
- “Moving Pictures” tutorial
- “Moving Pictures” tutorial - Multiple Interface Edition
- Fecal microbiota transplant (FMT) study: an exercise
- “Atacama soil microbiome” tutorial
- Parkinson’s Mouse Tutorial
- Importing data
- Exporting data
- Metadata in QIIME 2
- Filtering data
- Training feature classifiers with q2-feature-classifier
- Evaluating and controlling data quality with q2-quality-control
- Predicting sample metadata values with q2-sample-classifier
- Performing longitudinal and paired sample comparisons with q2-longitudinal
- Identifying and filtering chimeric feature sequences with q2-vsearch
- Alternative methods of read-joining in QIIME 2
- Clustering sequences into OTUs using q2-vsearch
- Utilities in QIIME 2
- Phylogenetic inference with q2-phylogeny
- Interfaces
- Plugins
- Semantic types
- Community
- Data resources
- Supplementary resources
- User Glossary
- Citing QIIME 2