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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 409

  2. augur augur Public

    Pipeline components for real-time phylodynamic analysis

    Python 275 135

  3. auspice auspice Public

    Web app for visualizing pathogen evolution

    JavaScript 304 168

Repositories

Showing 10 of 100 repositories
  • nextclade Public

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

    nextstrain/nextclade’s past year of commit activity
    TypeScript 250 MIT 66 120 (35 issues need help) 23 Updated Jan 10, 2026
  • rsv Public

    Workflow for RSV analyses on Nextstrain.org

    nextstrain/rsv’s past year of commit activity
    Python 10 6 10 5 Updated Jan 10, 2026
  • nextstrain.org Public

    The Nextstrain website

    nextstrain/nextstrain.org’s past year of commit activity
    JavaScript 96 AGPL-3.0 53 78 18 Updated Jan 10, 2026
  • augur Public

    Pipeline components for real-time phylodynamic analysis

    nextstrain/augur’s past year of commit activity
    Python 275 AGPL-3.0 135 233 (1 issue needs help) 37 Updated Jan 9, 2026
  • docs.nextstrain.org Public

    Umbrella documentation project for Nextstrain

    nextstrain/docs.nextstrain.org’s past year of commit activity
    Python 18 13 25 3 Updated Jan 9, 2026
  • seasonal-flu Public

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

    nextstrain/seasonal-flu’s past year of commit activity
    Python 56 29 33 9 Updated Jan 9, 2026
  • nextclade_data Public

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

    nextstrain/nextclade_data’s past year of commit activity
    Python 42 41 9 17 Updated Jan 9, 2026
  • measles Public

    Nextstrain build for measles virus

    nextstrain/measles’s past year of commit activity
    Python 3 8 5 8 Updated Jan 9, 2026
  • fauna Public

    RethinkDB database to support real-time virus analysis

    nextstrain/fauna’s past year of commit activity
    Python 35 AGPL-3.0 13 18 11 Updated Jan 8, 2026
  • auspice Public

    Web app for visualizing pathogen evolution

    nextstrain/auspice’s past year of commit activity
    JavaScript 304 AGPL-3.0 168 252 (4 issues need help) 40 Updated Jan 8, 2026
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