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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 2023.7 distribution in either scenario.


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:

QIIME 2 Core 2023.7 distribution

The QIIME 2 Core 2023.7 distribution includes the QIIME 2 framework, q2cli (a QIIME 2 command-line interface) and the following plugins:

  • q2-alignment

  • q2-composition

  • q2-cutadapt

  • q2-dada2

  • q2-deblur

  • q2-demux

  • q2-diversity

  • q2-diversity-lib

  • q2-emperor

  • q2-feature-classifier

  • q2-feature-table

  • q2-fragment-insertion

  • q2-gneiss

  • q2-longitudinal

  • q2-metadata

  • q2-phylogeny

  • q2-quality-control

  • q2-quality-filter

  • q2-sample-classifier

  • q2-taxa

  • q2-types

  • q2-vsearch


The QIIME 2 Core 2023.7 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.