The Nextstrain command-line tool, providing access to Nextstrain components in a local environment with a minimum of fuss.

Nextstrain CLI

This is the source code repository for a program called nextstrain, the Nextstrain command-line interface (CLI). It aims to provide a consistent way to run and visualize pathogen builds and access Nextstrain components like Augur and Auspice across computing environments such as Docker, Conda, and AWS Batch.

Get started using the Nextstrain CLI by reading the documentation, which includes installation and usage information.

If you'd like to contribute to development, the development docs should help you get going. We're glad you'd like to contribute!

If you need help (or just want to say hi!), open an issue or send us an email to