QIIME 2 Library (original) (raw)

Amplicon

A suite of plugins that provide broad analytic functionality to support microbiome marker gene analysis from raw sequencing data through publication quality visualizations and statistics.

Version

Links

Documentation Documentation

GitHub Source Code

Conda Channel

Built-in plugins

• q2
• q2-alignment
• q2-boots
• q2-composition
• q2-cutadapt
• q2-dada2
• q2-deblur
• q2-demux
• q2-diversity
• q2-diversity-lib
• q2-emperor
• q2-feature-classifier
• q2-feature-table
• q2-fondue
• q2-fragment-insertion
• q2-kmerizer
• q2-longitudinal
• q2-metadata
• q2-mystery-stew
• q2-phylogeny
• q2-quality-control
• q2-quality-filter
• q2-sample-classifier
• q2-stats
• q2-taxa
• q2-types
• q2-vizard
• q2-vsearch
• rachis
• RESCRIPt

Installation Instructions

You can install this distribution with either conda or docker.

Table of Contents

1. Using Conda
2. 1. Installing Miniconda
3. 2. Updating Miniconda
4. 3. Install the base distribution’s conda environment
5. 4. Test your install
6. Using Docker
7. 1. Install docker
8. 2. Download base image
9. 3. Test your install

Using Conda¶

Steps 1-4 will guide you through installing conda and your selected base distribution.

1. Installing Miniconda¶

Minicondaprovides the conda environment and package manager, and is the recommended way to install QIIME 2. Follow the Miniconda instructionsfor downloading and installing Miniconda. It is important to follow all of the directions provided in theMiniconda instructions, particularly ensuring that you run conda init at the end of the installation process (via installer or manual command), to ensure that your Miniconda installation is fully installed and available for the following commands.

2. Updating Miniconda¶

After installing Miniconda and opening a new terminal, make sure you’re running the latest version of conda:

3. Install the base distribution’s conda environment¶

We highly recommend creating a new environment specifically for the QIIME 2 distribution and release being installed, as there are many required dependencies that you may not want added to an existing environment.

You can choose whatever name you’d like for the environment. In this example, we’ll name the environments qiime2-amplicon-2026.1to indicate what QIIME 2 release is installed (i.e. 2026.1).

Instructions

Linux / Windows WSL

macOS (Apple Silicon)

macOS (Intel)

Select the tab that fits the operating system that you want QIIME 2 to run on.

(To install an older version, use the dropdown in the distribution details above.)

4. Test your install¶

Finally, to verify things are working, run:

conda deactivate
conda activate qiime2-amplicon-2026.1
qiime info

Using Docker¶

Steps 1-3 will guide you through installing docker and pulling the image for your selected base distribution.

1. Install docker¶

See https://www.docker.com for instructions for your platform.

2. Download base image¶

Run the following command to pull the selected image:

docker pull quay.io/qiime2/amplicon:2026.1

3. Test your install¶

Finally, to verify things are working, run:

docker run \
  -v $(pwd):/data \
  -it quay.io/qiime2/amplicon:2026.1 \
  qiime info

This command mounts your current working directory as a volume to /data inside the container, then starts an interactive session (-i) with the command qiime info using the image quay.io/qiime2/amplicon:2026.1 (-t).

Using Conda¶

Steps 1-4 will guide you through installing conda and your selected base distribution.

1. Installing Miniconda¶

Minicondaprovides the conda environment and package manager, and is the recommended way to install QIIME 2. Follow the Miniconda instructionsfor downloading and installing Miniconda. It is important to follow all of the directions provided in theMiniconda instructions, particularly ensuring that you run conda init at the end of the installation process (via installer or manual command), to ensure that your Miniconda installation is fully installed and available for the following commands.

2. Updating Miniconda¶

After installing Miniconda and opening a new terminal, make sure you’re running the latest version of conda:

3. Install the base distribution’s conda environment¶

We highly recommend creating a new environment specifically for the QIIME 2 distribution and release being installed, as there are many required dependencies that you may not want added to an existing environment.

You can choose whatever name you’d like for the environment. In this example, we’ll name the environments qiime2-amplicon-2026.1to indicate what QIIME 2 release is installed (i.e. 2026.1).

Instructions

Linux / Windows WSL

macOS (Apple Silicon)

macOS (Intel)

Select the tab that fits the operating system that you want QIIME 2 to run on.

(To install an older version, use the dropdown in the distribution details above.)

4. Test your install¶

Finally, to verify things are working, run:

conda deactivate
conda activate qiime2-amplicon-2026.1
qiime info

Using Docker¶

Steps 1-3 will guide you through installing docker and pulling the image for your selected base distribution.

1. Install docker¶

See https://www.docker.com for instructions for your platform.

2. Download base image¶

Run the following command to pull the selected image:

docker pull quay.io/qiime2/amplicon:2026.1

3. Test your install¶

Finally, to verify things are working, run:

docker run \
  -v $(pwd):/data \
  -it quay.io/qiime2/amplicon:2026.1 \
  qiime info

This command mounts your current working directory as a volume to /data inside the container, then starts an interactive session (-i) with the command qiime info using the image quay.io/qiime2/amplicon:2026.1 (-t).

Using Conda¶

Steps 1-4 will guide you through installing conda and your selected base distribution.

1. Installing Miniconda¶

Minicondaprovides the conda environment and package manager, and is the recommended way to install QIIME 2. Follow the Miniconda instructionsfor downloading and installing Miniconda. It is important to follow all of the directions provided in theMiniconda instructions, particularly ensuring that you run conda init at the end of the installation process (via installer or manual command), to ensure that your Miniconda installation is fully installed and available for the following commands.

2. Updating Miniconda¶

After installing Miniconda and opening a new terminal, make sure you’re running the latest version of conda:

3. Install the base distribution’s conda environment¶

We highly recommend creating a new environment specifically for the QIIME 2 distribution and release being installed, as there are many required dependencies that you may not want added to an existing environment.

You can choose whatever name you’d like for the environment. In this example, we’ll name the environments qiime2-amplicon-2026.1to indicate what QIIME 2 release is installed (i.e. 2026.1).

Instructions

Linux / Windows WSL

macOS (Apple Silicon)

macOS (Intel)

Select the tab that fits the operating system that you want QIIME 2 to run on.

(To install an older version, use the dropdown in the distribution details above.)

4. Test your install¶

Finally, to verify things are working, run:

conda deactivate
conda activate qiime2-amplicon-2026.1
qiime info

Using Docker¶

Steps 1-3 will guide you through installing docker and pulling the image for your selected base distribution.

1. Install docker¶

See https://www.docker.com for instructions for your platform.

2. Download base image¶

Run the following command to pull the selected image:

docker pull quay.io/qiime2/amplicon:2026.1

3. Test your install¶

Finally, to verify things are working, run:

docker run \
  -v $(pwd):/data \
  -it quay.io/qiime2/amplicon:2026.1 \
  qiime info

This command mounts your current working directory as a volume to /data inside the container, then starts an interactive session (-i) with the command qiime info using the image quay.io/qiime2/amplicon:2026.1 (-t).

Using Conda¶

Steps 1-4 will guide you through installing conda and your selected base distribution.

1. Installing Miniconda¶

Minicondaprovides the conda environment and package manager, and is the recommended way to install QIIME 2. Follow the Miniconda instructionsfor downloading and installing Miniconda. It is important to follow all of the directions provided in theMiniconda instructions, particularly ensuring that you run conda init at the end of the installation process (via installer or manual command), to ensure that your Miniconda installation is fully installed and available for the following commands.

2. Updating Miniconda¶

After installing Miniconda and opening a new terminal, make sure you’re running the latest version of conda:

3. Install the base distribution’s conda environment¶

We highly recommend creating a new environment specifically for the QIIME 2 distribution and release being installed, as there are many required dependencies that you may not want added to an existing environment.

You can choose whatever name you’d like for the environment. In this example, we’ll name the environments qiime2-amplicon-2026.1to indicate what QIIME 2 release is installed (i.e. 2026.1).

Instructions

Linux / Windows WSL

macOS (Apple Silicon)

macOS (Intel)

Select the tab that fits the operating system that you want QIIME 2 to run on.

(To install an older version, use the dropdown in the distribution details above.)

4. Test your install¶

Finally, to verify things are working, run:

conda deactivate
conda activate qiime2-amplicon-2026.1
qiime info

Using Docker¶

Steps 1-3 will guide you through installing docker and pulling the image for your selected base distribution.

1. Install docker¶

See https://www.docker.com for instructions for your platform.

2. Download base image¶

Run the following command to pull the selected image:

docker pull quay.io/qiime2/amplicon:2026.1

3. Test your install¶

Finally, to verify things are working, run:

docker run \
  -v $(pwd):/data \
  -it quay.io/qiime2/amplicon:2026.1 \
  qiime info

This command mounts your current working directory as a volume to /data inside the container, then starts an interactive session (-i) with the command qiime info using the image quay.io/qiime2/amplicon:2026.1 (-t).