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:
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:
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.