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.

Docker image build for nextstrain/base

Web app for visualizing pathogen evolution

Nextstrain build for measles virus

Narrative markdown files accessed via nextstrain.org/narratives/x

Scripts. config, and snakefiles for seasonal-flu nextstrain builds

Workflow for RSV analyses on Nextstrain.org

RethinkDB database to support real-time virus analysis

repository for workflows for various orthohantavirus builds

Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement