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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 279 137

  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 56 72 15 Updated Oct 3, 2026
  • augur Public

    Pipeline components for real-time phylodynamic analysis

    nextstrain/augur's past year of commit activity
    Python 279 AGPL-3.0 137 231 (1 issue needs help) 43 Updated Oct 2, 2026
  • ncov Public

    Nextstrain build for SARS-CoV-2

    nextstrain/ncov's past year of commit activity
    Python 1,362 MIT 408 69 19 Updated Oct 2, 2026
  • nextclade Public

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

    nextstrain/nextclade's past year of commit activity
    Rust 263 MIT 68 119 39 Updated Oct 2, 2026
  • shared Public

    Shared internal tooling for pathogen workflows. Used by our individual pathogen repos which produce Nextstrain builds.

    nextstrain/shared's past year of commit activity
    Python 1 1 4 4 Updated Oct 1, 2026
  • infra Public

    Nextstrain shared infrastructure

    nextstrain/infra's past year of commit activity
    Makefile 0 0 2 0 Updated Oct 1, 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 8 Updated Oct 1, 2026
  • forecasts-flu Public

    Seasonal influenza variant growth rates and frequency forecasts

    nextstrain/forecasts-flu's past year of commit activity
    Python 2 MIT 0 11 2 Updated Oct 1, 2026
  • nextclade_data Public

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

    nextstrain/nextclade_data's past year of commit activity
    Python 47 44 11 19 Updated Oct 1, 2026
  • ebola Public

    Nextstrain build for Ebola virus

    nextstrain/ebola's past year of commit activity
    Python 6 10 9 1 Updated Oct 1, 2026
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