Shared internal tooling for pathogen workflows. Used by our individual pathogen repos which produce Nextstrain builds.

A pipeline that ingests SARS-CoV-2 (i.e. nCoV) data from GISAID and Genbank, transforms it, stores it on S3, and triggers Nextstrain nCoV rebuilds.

Nextstrain build for Ebola virus

Conda package build for nextstrain-base

Nextstrain build for mpox virus

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.

A Sphinx theme for Nextstrain's documentation, based on Read The Docs' default theme.

Pipeline components for real-time phylodynamic analysis

SARS-CoV-2 variant growth rates and frequency forecasts