Installing QIIME 2¶
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This site has been replaced by the new QIIME 2 “amplicon distribution” documentation, as of the 2025.4 release of QIIME 2.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 Content on this site is no longer updated and may be out of date.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… 👴👵
QIIME 2 can be installed natively or using a virtual machine. The following pages describe how to install the available QIIME 2 2024.10 distributions in either scenario.
Recommendations¶
The native conda installation is generally the recommended method of installation, but this isn’t always available or a straight-forward option for all cases. In general we recommend the following:
macOS users
A native conda installation usually works well
Docker is a good backup option
Windows users
On newer versions of Windows, performing a native conda installation in the Windows Subsystem for Linux usually works well. See the WSL guide for instructions on how to set up the Windows Subsystem for Linux.
Docker is a good backup option
Linux users
A native conda installation usually works well
Docker is a good backup option
QIIME 2 2024.10 distributions¶
As of 2024.10, QIIME 2 releases now include the following QIIME 2 distributions that are available for install:
ampliconmetagenomepathogenometiny
QIIME 2 2024.10 Amplicon Distribution¶
The 2024.10 release of the QIIME 2 Amplicon Distribution includes the QIIME 2 framework, q2cli (a QIIME 2 command-line interface) and the following plugins:
q2-alignmentq2-compositionq2-cutadaptq2-dada2q2-deblurq2-demuxq2-diversityq2-diversity-libq2-emperorq2-feature-classifierq2-feature-tableq2-fragment-insertionq2-longitudinalq2-metadataq2-phylogenyq2-quality-controlq2-quality-filterq2-sample-classifierq2-taxaq2-typesq2-vsearchrescript
QIIME 2 2024.10 Metagenome Distribution¶
The 2024.10 release of the QIIME 2 Metagenome Distribution includes the QIIME 2 framework, q2cli (a QIIME 2 command-line interface) and the following plugins:
q2-assemblyq2-compositionq2-cutadaptq2-demuxq2-diversityq2-diversity-libq2-emperorq2-feature-classifierq2-feature-tableq2-fondueq2-longitudinalq2-metadataq2-moshpitq2-quality-controlq2-quality-filterq2-sample-classifierq2-sapiennsq2-taxaq2-typesq2-vsearchrescript
QIIME 2 2024.10 Pathogenome Distribution¶
The 2024.10 release of the QIIME 2 Metagenome Distribution includes the QIIME 2 framework, q2cli (a QIIME 2 command-line interface) and the following plugins:
q2-amrfinderplusq2-assemblyq2-demuxq2-feature-classifierq2-feature-tableq2-longitudinalq2-quality-controlq2-sample-classifierq2-taxaq2-typesq2-viromicsq2-vizardrescript
QIIME 2 2024.10 Tiny Distribution¶
The 2024.10 release of the QIIME 2 Tiny Distribution includes the QIIME 2 framework and q2cli (a QIIME 2 command-line interface) and the following plugins:
q2-types
The QIIME 2 Tiny Distribution is a minimal QIIME 2 environment that can be used by developers who are in need of a basic development environment, or community plugin users who do not need the entire Amplicon, Metagenome or Pathogenome Distributions in their QIIME 2 environment.
Note
The Amplicon Distribution is necessary to run the commands in the QIIME 2 tutorials. If there are additional QIIME 2 plugins or interfaces you would like to install, please consult the relevant package(s) documentation.