Nextstrain CLI
Warning
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.
Note
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: