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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 300 166

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 48 28 26 2 Updated Apr 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 65 4 Updated Apr 1, 2025
  • docs.nextstrain.org Public

    Umbrella documentation project for Nextstrain

    nextstrain/docs.nextstrain.org’s past year of commit activity
    Python 18 13 22 7 Updated Apr 1, 2025
  • nextclade_data Public

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

    nextstrain/nextclade_data’s past year of commit activity
    Python 33 27 9 15 Updated Mar 31, 2025
  • dengue Public

    Nextstrain build for dengue virus

    nextstrain/dengue’s past year of commit activity
    Python 8 12 13 (1 issue needs help) 0 Updated Mar 31, 2025
  • rsv Public

    Workflow for RSV analyses on Nextstrain.org

    nextstrain/rsv’s past year of commit activity
    Python 7 3 9 4 Updated Mar 31, 2025
  • nextstrain.org Public

    The Nextstrain website

    nextstrain/nextstrain.org’s past year of commit activity
    JavaScript 96 AGPL-3.0 50 69 14 Updated Mar 31, 2025
  • auspice Public

    Web app for visualizing pathogen evolution

    nextstrain/auspice’s past year of commit activity
    JavaScript 300 AGPL-3.0 166 234 (4 issues need help) 36 Updated Mar 31, 2025
  • nextclade Public

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

    nextstrain/nextclade’s past year of commit activity
    Rust 227 MIT 60 112 (31 issues need help) 22 Updated Mar 31, 2025
  • ebola Public

    Nextstrain build for Ebola virus

    nextstrain/ebola’s past year of commit activity
    Python 3 9 4 3 Updated Mar 29, 2025
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