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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
  • rsv Public

    Workflow for RSV analyses on Nextstrain.org

    nextstrain/rsv's past year of commit activity
    Python 11 8 9 3 Updated Oct 9, 2026
  • ncov Public

    Nextstrain build for SARS-CoV-2

    nextstrain/ncov's past year of commit activity
    Python 1,362 MIT 408 71 19 Updated Oct 9, 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 4 Updated Oct 9, 2026
  • infra Public

    Nextstrain shared infrastructure

    nextstrain/infra's past year of commit activity
    Makefile 0 0 2 1 Updated Oct 8, 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 8, 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 68 119 32 Updated Oct 8, 2026
  • auspice Public

    Web app for visualizing pathogen evolution

    nextstrain/auspice's past year of commit activity
    JavaScript 312 AGPL-3.0 172 251 (4 issues need help) 42 Updated Oct 8, 2026
  • nextstrain.org Public

    The Nextstrain website

    nextstrain/nextstrain.org's past year of commit activity
    JavaScript 96 AGPL-3.0 56 72 13 Updated Oct 7, 2026
  • .github Public
    nextstrain/.github's past year of commit activity
    Shell 9 11 12 0 Updated Oct 7, 2026
  • variant-nowcast-hub Public Forked from reichlab/variant-nowcast-hub

    A repository to store COVID-19 variant nowcasts collected as a modeling hub.

    nextstrain/variant-nowcast-hub's past year of commit activity
    R 0 MIT 18 0 0 Updated Oct 7, 2026
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