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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 406

  2. augur augur Public

    Pipeline components for real-time phylodynamic analysis

    Python 268 130

  3. auspice auspice Public

    Web app for visualizing pathogen evolution

    JavaScript 299 166

Repositories

Showing 10 of 94 repositories
  • seasonal-flu Public

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

    nextstrain/seasonal-flu’s past year of commit activity
    Python 47 27 28 0 Updated Mar 1, 2025
  • 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 27 MIT 20 62 5 Updated Mar 1, 2025
  • nextstrain.org Public

    The Nextstrain website

    nextstrain/nextstrain.org’s past year of commit activity
    JavaScript 95 AGPL-3.0 50 69 12 Updated Feb 28, 2025
  • mpox Public

    Nextstrain build for mpox virus

    nextstrain/mpox’s past year of commit activity
    Python 45 MIT 20 27 6 Updated Feb 28, 2025
  • forecasts-ncov Public

    SARS-CoV-2 variant growth rates and frequency forecasts

    nextstrain/forecasts-ncov’s past year of commit activity
    Python 7 2 11 6 Updated Feb 28, 2025
  • ncov-ingest Public

    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/ncov-ingest’s past year of commit activity
    Python 36 MIT 20 31 9 Updated Feb 28, 2025
  • ingest Public

    Shared internal tooling for pathogen data ingest. Used by our pathogen build repos.

    nextstrain/ingest’s past year of commit activity
    Shell 1 0 3 0 Updated Feb 28, 2025
  • WNV Public

    the repository used to build West Nile Virus for nextstrain

    nextstrain/WNV’s past year of commit activity
    Python 4 0 7 3 Updated Feb 28, 2025
  • lassa Public

    Nextstrain build for Lassa virus

    nextstrain/lassa’s past year of commit activity
    Python 0 5 11 1 Updated Feb 28, 2025
  • nextclade_data Public

    Datasets for https://github.com/nextstrain/nextclade

    nextstrain/nextclade_data’s past year of commit activity
    Python 33 27 8 14 Updated Feb 28, 2025
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