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