Nextstrain CLI


This is reference documentation for the Nextstrain CLI (command-line interface). If you’re just getting started with Nextstrain, please see our general documentation instead.

The Nextstrain CLI is a program called nextstrain. 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.


If you’re unfamiliar with Nextstrain builds, you may want to follow our Running a pathogen workflow tutorial first and then come back here.

Big Picture

The Nextstrain CLI glues together many different components. Below is a brief overview of the big picture:


Indices and Tables