This is an Augur-specific installation guide. If you wish to use Nextstrain as a whole, please refer to the Nextstrain installation guide.

Install Augur


There are some package managers that have entries with a similar name.

  • Augur on PyPI. This is a different project. Use nextstrain-augur instead.

  • augur on Debian. This is an unofficial version not maintained by the Nextstrain core team. It may lag behind official Augur releases. We do not generally recommend its use.

There are several ways to install Augur, ordered from least to most complex.

Augur is part of the Nextstrain project and is available in all Nextstrain runtimes.

Continue by following the Nextstrain installation guide.

Once installed, you can use nextstrain shell to run augur directly.

Testing if it worked

If installation worked, you should be able to run augur --help and see augur’s primary help output.