Repositories list

• nextclade_data

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

  Python

  •4242 forks•4545 stars•99 issues•1717 pull requests•Updated Apr 19, 2026Apr 19, 2026

• ncov-ingest

  Public

  nextstrain/ncov-ingest’s past year of commit activity
  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

  •2020 forks•3737 stars•3333 issues•1010 pull requests•Updated Apr 18, 2026Apr 18, 2026

• measles

  Public

  nextstrain/measles’s past year of commit activity
  Nextstrain build for measles virus

  pathogennextstrain

  pathogennextstrain

  Python

  •99 forks•33 stars•88 issues•88 pull requests•Updated Apr 17, 2026Apr 17, 2026

• auspice.us

  Public
  JavaScript

  •88 forks•1313 stars•55 issues•22 pull requests•Updated Apr 17, 2026Apr 17, 2026

• auspice

  Public

  nextstrain/auspice’s past year of commit activity
  Web app for visualizing pathogen evolution

  JavaScript

  •

  GNU Affero General Public License v3.0

  •171171 forks•309309 stars•252252 issues•3838 pull requests•Updated Apr 17, 2026Apr 17, 2026

• nextclade

  Public

  nextstrain/nextclade’s past year of commit activity
  Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement

  scienceresearchvirus+ 17

  scienceresearchvirussequencingnext-generation-sequencingdnarnainfluenzasequencesstrain+ 10

  TypeScript

  •

  MIT License

  •6666 forks•253253 stars•117117 issues•2929 pull requests•Updated Apr 17, 2026Apr 17, 2026

• rubella

  Public

  nextstrain/rubella’s past year of commit activity
  Nextstrain build for rubella virus

  pathogennextstrain

  pathogennextstrain

  Python

  •22 forks•22 stars•33 issues•33 pull requests•Updated Apr 16, 2026Apr 16, 2026

• shared

  Public

  nextstrain/shared’s past year of commit activity
  Shared internal tooling for pathogen workflows. Used by our individual pathogen repos which produce Nextstrain builds.

  Python

  •11 fork•11 star•55 issues•33 pull requests•Updated Apr 16, 2026Apr 16, 2026

• rsv

  Public

  nextstrain/rsv’s past year of commit activity
  Workflow for RSV analyses on Nextstrain.org

  pathogennextstrain

  pathogennextstrain

  Python

  •66 forks•1111 stars•99 issues•55 pull requests•Updated Apr 16, 2026Apr 16, 2026

• norovirus

  Public

  nextstrain/norovirus’s past year of commit activity
  pathogennextstrain

  pathogennextstrain

  Python

  •

  MIT License

  •11 fork•33 stars•88 issues•22 pull requests•Updated Apr 16, 2026Apr 16, 2026

• yellow-fever

  Public
  pathogennextstrain

  pathogennextstrain

  Python

  •55 forks•22 stars•00 issues•11 pull request•Updated Apr 16, 2026Apr 16, 2026

• lassa

  Public
  Nextstrain build for Lassa virus

  pathogennextstrain

  pathogennextstrain

  Python

  •55 forks•44 stars•99 issues•33 pull requests•Updated Apr 16, 2026Apr 16, 2026

• chikv

  Public
  Chikungunya virus workflows

  pathogennextstrain

  pathogennextstrain

  Python

  •00 forks•11 star•00 issues•11 pull request•Updated Apr 16, 2026Apr 16, 2026

• mpox

  Public

  nextstrain/mpox’s past year of commit activity
  Nextstrain build for mpox virus

  metadatabioinformaticspipeline+ 10

  metadatabioinformaticspipelinepathogenphylogeneticsgenbankaugurnextstrainauspicevirus-evolution+ 3

  Python

  •

  MIT License

  •2222 forks•5050 stars•1717 issues•99 pull requests•Updated Apr 16, 2026Apr 16, 2026

• seasonal-cov

  Public
  Nextstrain build for seasonal coronaviruses

  pathogennextstrain

  pathogennextstrain

  Python

  •00 forks•11 star•11 issue•11 pull request•Updated Apr 16, 2026Apr 16, 2026

• dengue

  Public

  nextstrain/dengue’s past year of commit activity
  Nextstrain build for dengue virus

  pathogennextstrain

  pathogennextstrain

  Python

  •1212 forks•1414 stars•1717 issues•22 pull requests•Updated Apr 16, 2026Apr 16, 2026

• zika

  Public
  Nextstrain build for Zika virus

  pathogennextstrain

  pathogennextstrain

  Python

  •1111 forks•1010 stars•55 issues•33 pull requests•Updated Apr 16, 2026Apr 16, 2026

• forecasts-ncov

  Public
  SARS-CoV-2 variant growth rates and frequency forecasts

  bioinformaticspathogenforecasts+ 4

  bioinformaticspathogenforecastsnextstrainsars-cov-2pango-lineagessars-cov-2-variants

  Python

  •33 forks•99 stars•1212 issues•44 pull requests•Updated Apr 16, 2026Apr 16, 2026

• mumps

  Public
  Nextstrain build for mumps virus

  pathogennextstrain

  pathogennextstrain

  Python

  •77 forks•22 stars•55 issues•44 pull requests•Updated Apr 16, 2026Apr 16, 2026

• WNV

  Public
  the repository used to build West Nile Virus for nextstrain

  pathogennextstrain

  pathogennextstrain

  Python

  •33 forks•55 stars•77 issues•22 pull requests•Updated Apr 16, 2026Apr 16, 2026

• avian-flu

  Public

  nextstrain/avian-flu’s past year of commit activity
  Nextstrain build for avian influenza viruses

  pathogennextstrain

  pathogennextstrain

  Python

  •1010 forks•2727 stars•1818 issues•77 pull requests•Updated Apr 16, 2026Apr 16, 2026

• rabies

  Public
  pathogennextstrain

  pathogennextstrain

  Python

  •11 fork•00 stars•55 issues•11 pull request•Updated Apr 16, 2026Apr 16, 2026

• pathogen-repo-guide

  Public template
  Python

  •11 fork•44 stars•2424 issues•11 pull request•Updated Apr 16, 2026Apr 16, 2026

• docker-base

  Public
  Docker image build for nextstrain/base

  Shell

  •77 forks•1212 stars•77 issues•11 pull request•Updated Apr 15, 2026Apr 15, 2026

• nextstrain.org

  Public
  The Nextstrain website

  JavaScript

  •

  GNU Affero General Public License v3.0

  •5454 forks•9696 stars•7070 issues•1111 pull requests•Updated Apr 15, 2026Apr 15, 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•6868 issues•33 pull requests•Updated Apr 15, 2026Apr 15, 2026

• ebola

  Public
  Nextstrain build for Ebola virus

  pathogennextstrain

  pathogennextstrain

  Python

  •99 forks•44 stars•88 issues•22 pull requests•Updated Apr 15, 2026Apr 15, 2026

• hmpv

  Public
  Human metapneumovirus pathogen build

  pathogennextstrain

  pathogennextstrain

  Python

  •00 forks•00 stars•55 issues•11 pull request•Updated Apr 15, 2026Apr 15, 2026

• seasonal-flu

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

  pathogennextstrain

  pathogennextstrain

  Python

  •3131 forks•5959 stars•2727 issues•88 pull requests•Updated Apr 15, 2026Apr 15, 2026

• oropouche

  Public
  Oropouche Nextstrain build

  pathogennextstrain

  pathogennextstrain

  Python

  •22 forks•11 star•00 issues•11 pull request•Updated Apr 15, 2026Apr 15, 2026