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@nextstrain

Nextstrain

Real-time tracking of pathogen evolution

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  1. ncov ncov Public

    Nextstrain build for SARS-CoV-2

    Python 1.4k 408

  2. augur augur Public

    Pipeline components for real-time phylodynamic analysis

    Python 280 139

  3. auspice auspice Public

    Web app for visualizing pathogen evolution

    JavaScript 312 172

Repositories

Showing 10 of 105 repositories
  • nextstrain.org Public

    The Nextstrain website

    nextstrain/nextstrain.org's past year of commit activity
    JavaScript 96 AGPL-3.0 58 70 13 Updated Oct 30, 2026
  • seasonal-flu Public

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

    nextstrain/seasonal-flu's past year of commit activity
    Python 65 34 28 10 Updated Oct 30, 2026
  • rsv Public

    Workflow for RSV analyses on Nextstrain.org

    nextstrain/rsv's past year of commit activity
    Python 11 8 9 4 Updated Oct 30, 2026
  • WNV Public

    the repository used to build West Nile Virus for nextstrain

    nextstrain/WNV's past year of commit activity
    Python 5 3 7 1 Updated Oct 30, 2026
  • auspice Public

    Web app for visualizing pathogen evolution

    nextstrain/auspice's past year of commit activity
    JavaScript 312 AGPL-3.0 172 246 (4 issues need help) 42 Updated Oct 30, 2026
  • augur Public

    Pipeline components for real-time phylodynamic analysis

    nextstrain/augur's past year of commit activity
    Python 280 AGPL-3.0 139 229 (1 issue needs help) 42 Updated Oct 30, 2026
  • ebola Public

    Nextstrain build for Ebola virus

    nextstrain/ebola's past year of commit activity
    Python 7 11 12 2 Updated Oct 30, 2026
  • auspice.us Public
    nextstrain/auspice.us's past year of commit activity
    JavaScript 13 8 4 0 Updated Oct 29, 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 71 6 Updated Oct 29, 2026
  • bioconda-recipes Public Forked from bioconda/bioconda-recipes

    Fork for maintaining Nextstrain-related recipes and submitting PRs upstream.

    nextstrain/bioconda-recipes's past year of commit activity
    Shell 0 4,205 3 0 Updated Oct 29, 2026
View all repositories