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.
Table of Contents
- AWS Batch
The Nextstrain CLI glues together many different components. Below is a brief overview of the big picture: