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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
  • nextclade_data Public

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

    nextstrain/nextclade_data's past year of commit activity
    Python 47 44 11 20 Updated Oct 24, 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 27 9 Updated Oct 24, 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 23, 2026
  • augur Public

    Pipeline components for real-time phylodynamic analysis

    nextstrain/augur's past year of commit activity
    Python 280 AGPL-3.0 139 230 (1 issue needs help) 42 Updated Oct 23, 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 72 7 Updated Oct 23, 2026
  • nextclade Public

    Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement

    nextstrain/nextclade's past year of commit activity
    Rust 265 MIT 69 119 31 Updated Oct 23, 2026
  • nextstrain.org Public

    The Nextstrain website

    nextstrain/nextstrain.org's past year of commit activity
    JavaScript 96 AGPL-3.0 58 70 14 Updated Oct 23, 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 4,192 3 0 Updated Oct 22, 2026
  • enterovirus_d68 Public

    Enterovirus-D68 phylogenetic analyses code - actively maintained

    nextstrain/enterovirus_d68's past year of commit activity
    Python 1 6 1 0 Updated Oct 22, 2026
  • conda-base Public

    Conda package build for nextstrain-base

    nextstrain/conda-base's past year of commit activity
    Shell 1 1 4 1 Updated Oct 22, 2026
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