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@nextstrain

Nextstrain

Real-time tracking of pathogen evolution

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  1. ncov Public

    Nextstrain build for SARS-CoV-2

    Python 1.4k 406

  2. augur Public

    Pipeline components for real-time phylodynamic analysis

    Python 268 130

  3. auspice Public

    Web app for visualizing pathogen evolution

    JavaScript 300 166

Repositories

Showing 10 of 94 repositories
  • nextclade Public

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

    Rust 227 MIT 60 110 (31 issues need help) 19 Updated Apr 1, 2025
  • nextclade_data Public

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

    Python 33 27 9 14 Updated Apr 1, 2025
  • seasonal-flu Public

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

    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.

    Python 27 MIT 20 65 4 Updated Apr 1, 2025
  • docs.nextstrain.org Public

    Umbrella documentation project for Nextstrain

    Python 18 13 22 7 Updated Apr 1, 2025
  • dengue Public

    Nextstrain build for dengue virus

    Python 8 12 13 (1 issue needs help) 0 Updated Mar 31, 2025
  • rsv Public

    Workflow for RSV analyses on Nextstrain.org

    Python 7 3 9 4 Updated Mar 31, 2025
  • nextstrain.org Public

    The Nextstrain website

    JavaScript 96 AGPL-3.0 50 69 14 Updated Mar 31, 2025
  • auspice Public

    Web app for visualizing pathogen evolution

    JavaScript 300 AGPL-3.0 166 234 (4 issues need help) 36 Updated Mar 31, 2025
  • ebola Public

    Nextstrain build for Ebola virus

    Python 3 9 4 3 Updated Mar 29, 2025
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