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 computing platforms, such as Docker runtime, Conda runtime, Singularity runtime, and AWS Batch runtime.


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

Table of Contents



Big Picture

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


Indices and Tables