Nextstrain

Real-time tracking of pathogen evolution

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ncov ncov Public

Nextstrain build for SARS-CoV-2

Python 1.4k 409
augur augur Public

Pipeline components for real-time phylodynamic analysis

Python 276 136
auspice auspice Public

Web app for visualizing pathogen evolution

JavaScript 307 169

Repositories

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

nextstrain/seasonal-flu’s past year of commit activity

Python 59 29 29 9 Updated Mar 20, 2026
cli Public
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.

nextstrain/cli’s past year of commit activity

Python 28 MIT 20 69 5 Updated Mar 20, 2026
.github Public

nextstrain/.github’s past year of commit activity

Shell 9 11 11 1 Updated Mar 20, 2026
docker-base Public
Docker image build for nextstrain/base

nextstrain/docker-base’s past year of commit activity

Shell 12 7 7 1 Updated Mar 19, 2026
variant-nowcast-hub Public Forked from reichlab/variant-nowcast-hub
A repository to store COVID-19 variant nowcasts collected as a modeling hub.

nextstrain/variant-nowcast-hub’s past year of commit activity

R 0 MIT 17 0 0 Updated Mar 18, 2026
nextstrain.org Public
The Nextstrain website

nextstrain/nextstrain.org’s past year of commit activity

JavaScript 96 AGPL-3.0 54 70 11 Updated Mar 18, 2026
docs.nextstrain.org Public
Umbrella documentation project for Nextstrain

nextstrain/docs.nextstrain.org’s past year of commit activity

Python 18 13 24 4 Updated Mar 17, 2026
augur Public
Pipeline components for real-time phylodynamic analysis

nextstrain/augur’s past year of commit activity

Python 276 AGPL-3.0 136 232 (1 issue needs help) 38 Updated Mar 17, 2026
conda-base Public
Conda package build for nextstrain-base

nextstrain/conda-base’s past year of commit activity

Shell 1 1 5 1 Updated Mar 17, 2026
rsv Public
Workflow for RSV analyses on Nextstrain.org

nextstrain/rsv’s past year of commit activity

Python 11 6 9 4 Updated Mar 17, 2026