Getting started¶
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This site has been replaced by the new QIIME 2 “amplicon distribution” documentation, as of the 2025.4 release of QIIME 2.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 Content on this site is no longer updated and may be out of date.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… 👴👵
This guide will walk you through the steps necessary to understand, install, and use QIIME 2 for your own microbiome analyses:
Familiarize yourself with the core concepts of QIIME 2 before starting to use the system.
Work through the tutorials to learn how to use QIIME 2 to perform microbiome analyses. We recommend starting with the grand overview and Moving Pictures tutorial, followed by the FMT study and Atacama Desert soils tutorials.
Try out other interfaces. QIIME 2 supports multiple user interfaces, and you’ve only been exposed to q2cli, a command line interface, so far. If you are interested in using a different interface for your QIIME 2 analyses, explore the interfaces that are currently available. For example, check out the Artifact API if you are wanting to use a Python 3 API optimized for the Jupyter Notebook.