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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 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:

QIIME 2 2024.10 distributions

As of 2024.10, QIIME 2 releases now include the following QIIME 2 distributions that are available for install:

  • amplicon

  • metagenome

  • pathogenome

  • tiny

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-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-longitudinal

  • q2-metadata

  • q2-phylogeny

  • q2-quality-control

  • q2-quality-filter

  • q2-sample-classifier

  • q2-taxa

  • q2-types

  • q2-vsearch

  • rescript

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-assembly

  • q2-composition

  • q2-cutadapt

  • q2-demux

  • q2-diversity

  • q2-diversity-lib

  • q2-emperor

  • q2-feature-classifier

  • q2-feature-table

  • q2-fondue

  • q2-longitudinal

  • q2-metadata

  • q2-moshpit

  • q2-quality-control

  • q2-quality-filter

  • q2-sample-classifier

  • q2-sapienns

  • q2-taxa

  • q2-types

  • q2-vsearch

  • rescript

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-amrfinderplus

  • q2-assembly

  • q2-demux

  • q2-feature-classifier

  • q2-feature-table

  • q2-longitudinal

  • q2-quality-control

  • q2-sample-classifier

  • q2-taxa

  • q2-types

  • q2-viromics

  • q2-vizard

  • rescript

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.