Installing QIIME 2¶
QIIME 2 can be installed natively or using a virtual machine. The following pages describe how to install the QIIME 2 Core 2023.5 distribution 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 Core 2023.5 distribution¶
The QIIME 2 Core 2023.5 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-gneissq2-longitudinalq2-metadataq2-phylogenyq2-quality-controlq2-quality-filterq2-sample-classifierq2-taxaq2-typesq2-vsearch
Note
The QIIME 2 Core 2023.5 distribution includes plugins and interfaces that are developed, maintained, tested, and distributed by the QIIME 2 development team. The Core 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. Other types of distributions may be made available in the future in addition to Core.