Repositories list

• seasonal-flu

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

  pathogennextstrain

  pathogennextstrain

  Python

  •3434 forks•6464 stars•2727 issues•99 pull requests•Updated Sep 10, 2026Sep 10, 2026

• status

  Public
  Nextstrain status pages

  JavaScript

  •

  MIT License

  •11 fork•11 star•44 issues•00 pull requests•Updated Sep 10, 2026Sep 10, 2026

• real-time-pathogens-ms

  Public
  Nextstrain automates real-time phylogenetic analysis of open data for endemic and emerging pathogens

  TeX

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 10, 2026Sep 10, 2026

• ebola

  Public
  Nextstrain build for Ebola virus

  pathogennextstrain

  pathogennextstrain

  Python

  •1010 forks•66 stars•99 issues•00 pull requests•Updated Sep 9, 2026Sep 9, 2026

• bioconda-recipes

  Public
  Fork for maintaining Nextstrain-related recipes and submitting PRs upstream.

  Shell

  •4.1k4.1k forks•00 stars•33 issues•00 pull requests•Updated Sep 9, 2026Sep 9, 2026

• augur

  Public
  Pipeline components for real-time phylodynamic analysis

  Python

  •

  GNU Affero General Public License v3.0

  •135135 forks•279279 stars•230230 issues•3737 pull requests•Updated Sep 9, 2026Sep 9, 2026

• variant-nowcast-hub

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

  R

  •

  MIT License

  •1717 forks•00 stars•00 issues•00 pull requests•Updated Sep 9, 2026Sep 9, 2026

• forecasts-flu

  Public
  Seasonal influenza variant growth rates and frequency forecasts

  pathogennextstrain

  pathogennextstrain

  Python

  •

  MIT License

  •00 forks•11 star•1111 issues•44 pull requests•Updated Sep 8, 2026Sep 8, 2026

• shared

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

  Python

  •11 fork•11 star•44 issues•55 pull requests•Updated Sep 8, 2026Sep 8, 2026

• nextstrain.org

  Public
  The Nextstrain website

  JavaScript

  •

  GNU Affero General Public License v3.0

  •5656 forks•9696 stars•7070 issues•1212 pull requests•Updated Sep 8, 2026Sep 8, 2026

• nextclade_data

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

  Python

  •4343 forks•4747 stars•1111 issues•1818 pull requests•Updated Sep 7, 2026Sep 7, 2026

• auspice

  Public
  Web app for visualizing pathogen evolution

  JavaScript

  •

  GNU Affero General Public License v3.0

  •171171 forks•312312 stars•250250 issues•4141 pull requests•Updated Sep 7, 2026Sep 7, 2026

• measles

  Public
  Nextstrain build for measles virus

  pathogennextstrain

  pathogennextstrain

  Python

  •99 forks•44 stars•77 issues•22 pull requests•Updated Sep 4, 2026Sep 4, 2026

• docker-base

  Public
  Docker image build for nextstrain/base

  Shell

  •88 forks•1212 stars•77 issues•11 pull request•Updated Sep 4, 2026Sep 4, 2026

• .github

  Public
  Shell

  •1111 forks•99 stars•1313 issues•00 pull requests•Updated Sep 3, 2026Sep 3, 2026

• auspice.us

  Public
  JavaScript

  •88 forks•1313 stars•44 issues•00 pull requests•Updated Sep 2, 2026Sep 2, 2026

• narratives

  Public
  Narrative markdown files accessed via nextstrain.org/narratives/x

  Shell

  •1010 forks•33 stars•22 issues•11 pull request•Updated Sep 2, 2026Sep 2, 2026

• rsv

  Public
  Workflow for RSV analyses on Nextstrain.org

  pathogennextstrain

  pathogennextstrain

  Python

  •77 forks•1111 stars•1010 issues•44 pull requests•Updated Aug 28, 2026Aug 28, 2026

• mpox

  Public
  Nextstrain build for mpox virus

  metadatabioinformaticspipeline+ 10

  metadatabioinformaticspipelinepathogenphylogeneticsgenbankaugurnextstrainauspicevirus-evolution+ 3

  Python

  •

  MIT License

  •2222 forks•5050 stars•1919 issues•88 pull requests•Updated Aug 27, 2026Aug 27, 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 N…

  Python

  •

  MIT License

  •2020 forks•2828 stars•7171 issues•44 pull requests•Updated Aug 26, 2026Aug 26, 2026

• fauna

  Public
  RethinkDB database to support real-time virus analysis

  Python

  •

  GNU Affero General Public License v3.0

  •1212 forks•3636 stars•1919 issues•1010 pull requests•Updated Aug 20, 2026Aug 20, 2026

• nextclade

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

  scienceresearchvirus+ 17

  scienceresearchvirussequencingnext-generation-sequencingdnarnainfluenzasequencesstrain+ 10

  Rust

  •

  MIT License

  •6767 forks•262262 stars•119119 issues•3333 pull requests•Updated Aug 19, 2026Aug 19, 2026

• docs.nextstrain.org

  Public
  Umbrella documentation project for Nextstrain

  Python

  •1313 forks•1818 stars•2626 issues•22 pull requests•Updated Aug 18, 2026Aug 18, 2026

• ncov

  Public
  Nextstrain build for SARS-CoV-2

  pathogennextstrainncov+ 1

  pathogennextstrainncovsars-cov-2

  Python

  •

  MIT License

  •408408 forks•1.4k1.4k stars•7272 issues•2020 pull requests•Updated Aug 17, 2026Aug 17, 2026

• newcastle-disease-virus

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 15, 2026Aug 15, 2026

• hantavirus

  Public
  repository for workflows for various orthohantavirus builds

  pathogennextstrain

  pathogennextstrain

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 13, 2026Aug 13, 2026

• andv

  Public
  Andes hantavirus

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 9, 2026Aug 9, 2026

• rubella

  Public
  Nextstrain build for rubella virus

  pathogennextstrain

  pathogennextstrain

  Python

  •22 forks•22 stars•33 issues•22 pull requests•Updated Aug 7, 2026Aug 7, 2026

• ncov-ingest

  Public
  A pipeline that ingests SARS-CoV-2 (i.e. nCoV) data from GISAID and Genbank, transforms it, stores it on S3, and triggers Nextstrain nCoV rebuilds.

  pythonbashpathogen+ 5

  pythonbashpathogengenbanknextstrainncovsars-cov-2gisaid

  Python

  •

  MIT License

  •2121 forks•3737 stars•3131 issues•1010 pull requests•Updated Aug 5, 2026Aug 5, 2026

• zika

  Public
  Nextstrain build for Zika virus

  pathogennextstrain

  pathogennextstrain

  Python

  •1111 forks•1111 stars•55 issues•33 pull requests•Updated Aug 3, 2026Aug 3, 2026