Skip to content
@nextstrain

Nextstrain

Real-time tracking of pathogen evolution

Pinned Loading

  1. ncov ncov Public

    Nextstrain build for SARS-CoV-2

    Python 1.4k 409

  2. augur augur Public

    Pipeline components for real-time phylodynamic analysis

    Python 275 135

  3. auspice auspice Public

    Web app for visualizing pathogen evolution

    JavaScript 305 169

Repositories

Showing 10 of 100 repositories
  • nextstrain.org Public

    The Nextstrain website

    nextstrain/nextstrain.org’s past year of commit activity
    JavaScript 96 AGPL-3.0 54 74 13 Updated Feb 24, 2026
  • seasonal-flu Public

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

    nextstrain/seasonal-flu’s past year of commit activity
    Python 58 29 31 9 Updated Feb 23, 2026
  • rsv Public

    Workflow for RSV analyses on Nextstrain.org

    nextstrain/rsv’s past year of commit activity
    Python 11 7 9 5 Updated Feb 21, 2026
  • measles Public

    Nextstrain build for measles virus

    nextstrain/measles’s past year of commit activity
    Python 3 8 5 8 Updated Feb 21, 2026
  • augur Public

    Pipeline components for real-time phylodynamic analysis

    nextstrain/augur’s past year of commit activity
    Python 275 AGPL-3.0 135 233 (1 issue needs help) 40 Updated Feb 21, 2026
  • WNV Public

    the repository used to build West Nile Virus for nextstrain

    nextstrain/WNV’s past year of commit activity
    Python 5 3 8 3 Updated Feb 21, 2026
  • forecasts-flu Public

    Seasonal influenza variant growth rates and frequency forecasts

    nextstrain/forecasts-flu’s past year of commit activity
    Python 1 MIT 0 10 1 Updated Feb 20, 2026
  • fauna Public

    RethinkDB database to support real-time virus analysis

    nextstrain/fauna’s past year of commit activity
    Python 35 AGPL-3.0 12 18 11 Updated Feb 19, 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 70 4 Updated Feb 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 Feb 18, 2026
View all repositories