Nextstrain CLI


This is the Nextstrain CLI’s reference documentation. For the general Nextstrain docs, go here: Welcome to Nextstrain’s documentation!

This is the documentation for the Nextstrain command-line interface (CLI)—a program called nextstrain—which 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 quickstart guide 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