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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 275 136

  3. auspice auspice Public

    Web app for visualizing pathogen evolution

    JavaScript 305 168

Repositories

Showing 10 of 100 repositories
  • augur Public

    Pipeline components for real-time phylodynamic analysis

    nextstrain/augur’s past year of commit activity
    Python 275 AGPL-3.0 136 234 (1 issue needs help) 41 Updated Feb 14, 2026
  • seasonal-flu Public

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

    nextstrain/seasonal-flu’s past year of commit activity
    Python 57 29 31 9 Updated Feb 13, 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 5 Updated Feb 13, 2026
  • yellow-fever Public
    nextstrain/yellow-fever’s past year of commit activity
    Python 2 4 0 0 Updated Feb 13, 2026
  • rsv Public

    Workflow for RSV analyses on Nextstrain.org

    nextstrain/rsv’s past year of commit activity
    Python 10 7 9 5 Updated Feb 13, 2026
  • avian-flu Public

    Nextstrain build for avian influenza viruses

    nextstrain/avian-flu’s past year of commit activity
    Python 27 10 18 6 Updated Feb 13, 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 3,768 3 0 Updated Feb 12, 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 Feb 12, 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 2 Updated Feb 12, 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 8 1 Updated Feb 11, 2026
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