Getting started

The tutorials in Using QIIME 2 provide basic information on how to use the QIIME 2 framework, q2cli (i.e., the official QIIME 2 command line interface), and the QIIME 2 Python 3 API. The tutorials make use of the Tiny Distribution, and the QIIME 2 example plugin q2-dwq2. This deployment allows for in-depth learning of how QIIME 2 itself works, and the information you learn here will be relevant across all QIIME 2 distributions. When you’re ready to perform your own data analysis you’ll transition to domain-specific plugins or distributions and their documentation.

Before attempting to run the Using QIIME 2 tutorials, configure your learning environment following the steps here.

Install the QIIME 2 “Tiny Distribution”¶

The QIIME 2 “Tiny Distribution” is a minimal set of QIIME 2 functionality for building and using plugins through the QIIME 2 command line or Python 3 API. Install the most recent release version of the QIIME 2 Tiny Distribution using the instructions on the QIIME 2 Library.

Activate the conda environment and test your installation¶

You can now activate the environment you just created using conda activate, as described in the installation instructions.

To test your QIIME 2 environment, run:

qiime info

You should see something like the following, though the version numbers you’ll see may be different:

System versions
Python version: 3.10.14
QIIME 2 release: 2025.4
QIIME 2 version: 2025.4.0
q2cli version: 2025.4.0

Installed plugins
metadata: 2025.4.0
types: 2025.4.0

...

At this stage you have a working QIIME 2 environment, but it doesn’t do a whole lot. To add some bioinformatics functionality, we’ll next add the QIIME 2 example plugin q2-dwq2.

Install q2-dwq2¶

All domain-specific functionality in QIIME 2 comes in the form of plugins. Sometimes you’ll install these directly, and sometimes you’ll install QIIME 2 distributions which are bundles of plugins intended to be used together. In this case, we’re going to install one specific plugin. Run the following command from your using-qiime2 conda environment (i.e., after having run conda activate using-qiime2).

pip install https://github.com/caporaso-lab/q2-dwq2/archive/refs/heads/main.zip

If you run qiime info again, you should now see a new plugin, dwq2, in the list of Installed Plugins.

System versions
Python version: 3.10.14
QIIME 2 release: 2025.4
QIIME 2 version: 2025.4.0
q2cli version: 2025.4.0

Installed plugins
dwq2: 0+unknown
metadata: 2025.4.0
types: 2025.4.0

...

Exploring the available functionality¶

To see the list of available plugins, along with some additional information, run:

qiime --help

To see what functionality, or Actions a plugin defines, call help on that plugin:

qiime dwq2 --help

To learn how to use a specific action, call help on it:

qiime dwq2 nw-align --help

Take a few minutes now to explore q2-dwq2. What is this plugin intended to do? What is some of the functionality that it provides?