Installing QIIME 2¶
QIIME 2 can be installed natively or using virtual machines. The following pages describe how to install the QIIME 2 Core 2020.11 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 and VirtualBox are good backup options
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 and VirtualBox are good backup options
Linux users
A native conda installation usually works well
Docker and VirtualBox are good backup options
QIIME 2 Core 2020.11 distribution¶
The QIIME 2 Core 2020.11 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 2020.11 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.