Repositories list

• nextclade_data

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

  Python

  •4242 forks•4545 stars•1010 issues•1616 pull requests•Updated Apr 25, 2026Apr 25, 2026

• nextclade

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

  scienceresearchvirus+ 17

  scienceresearchvirussequencingnext-generation-sequencingdnarnainfluenzasequencesstrain+ 10

  TypeScript

  •

  MIT License

  •6767 forks•253253 stars•117117 issues•2929 pull requests•Updated Apr 25, 2026Apr 25, 2026

• auspice

  Public
  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 25, 2026Apr 25, 2026

• seasonal-flu

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

  pathogennextstrain

  pathogennextstrain

  Python

  •3131 forks•5959 stars•2727 issues•99 pull requests•Updated Apr 25, 2026Apr 25, 2026

• forecasts-flu

  Public
  Seasonal influenza variant growth rates and frequency forecasts

  pathogennextstrain

  pathogennextstrain

  Python

  •

  MIT License

  •00 forks•11 star•1111 issues•22 pull requests•Updated Apr 24, 2026Apr 24, 2026

• auspice.us

  Public
  JavaScript

  •88 forks•1313 stars•55 issues•22 pull requests•Updated Apr 23, 2026Apr 23, 2026

• docs.nextstrain.org

  Public
  Umbrella documentation project for Nextstrain

  Python

  •1313 forks•1818 stars•2424 issues•44 pull requests•Updated Apr 23, 2026Apr 23, 2026

• augur

  Public
  Pipeline components for real-time phylodynamic analysis

  Python

  •

  GNU Affero General Public License v3.0

  •136136 forks•276276 stars•232232 issues•3636 pull requests•Updated Apr 22, 2026Apr 22, 2026

• variant-nowcast-hub

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

  R

  •

  MIT License

  •1515 forks•00 stars•00 issues•00 pull requests•Updated Apr 22, 2026Apr 22, 2026

• measles

  Public
  Nextstrain build for measles virus

  pathogennextstrain

  pathogennextstrain

  Python

  •99 forks•33 stars•77 issues•66 pull requests•Updated Apr 21, 2026Apr 21, 2026

• conda-base

  Public
  Conda package build for nextstrain-base

  condamambanextstrain

  condamambanextstrain

  Shell

  •11 fork•11 star•44 issues•11 pull request•Updated Apr 21, 2026Apr 21, 2026

• yellow-fever

  Public
  pathogennextstrain

  pathogennextstrain

  Python

  •55 forks•22 stars•00 issues•00 pull requests•Updated Apr 20, 2026Apr 20, 2026

• zika

  Public
  Nextstrain build for Zika virus

  pathogennextstrain

  pathogennextstrain

  Python

  •1111 forks•1010 stars•55 issues•22 pull requests•Updated Apr 20, 2026Apr 20, 2026

• seasonal-cov

  Public
  Nextstrain build for seasonal coronaviruses

  pathogennextstrain

  pathogennextstrain

  Python

  •00 forks•11 star•11 issue•00 pull requests•Updated Apr 20, 2026Apr 20, 2026

• rubella

  Public
  Nextstrain build for rubella virus

  pathogennextstrain

  pathogennextstrain

  Python

  •22 forks•22 stars•33 issues•22 pull requests•Updated Apr 20, 2026Apr 20, 2026

• rsv

  Public
  Workflow for RSV analyses on Nextstrain.org

  pathogennextstrain

  pathogennextstrain

  Python

  •66 forks•1111 stars•99 issues•44 pull requests•Updated Apr 20, 2026Apr 20, 2026

• rabies

  Public
  pathogennextstrain

  pathogennextstrain

  Python

  •11 fork•00 stars•55 issues•00 pull requests•Updated Apr 20, 2026Apr 20, 2026

• pathogen-repo-guide

  Public template
  Python

  •11 fork•44 stars•2424 issues•00 pull requests•Updated Apr 20, 2026Apr 20, 2026

• oropouche

  Public
  Oropouche Nextstrain build

  pathogennextstrain

  pathogennextstrain

  Python

  •22 forks•11 star•00 issues•00 pull requests•Updated Apr 20, 2026Apr 20, 2026

• norovirus

  Public
  pathogennextstrain

  pathogennextstrain

  Python

  •

  MIT License

  •11 fork•33 stars•99 issues•11 pull request•Updated Apr 20, 2026Apr 20, 2026

• nipah

  Public
  pathogennextstrain

  pathogennextstrain

  Python

  •00 forks•22 stars•22 issues•00 pull requests•Updated Apr 20, 2026Apr 20, 2026

• mumps

  Public
  Nextstrain build for mumps virus

  pathogennextstrain

  pathogennextstrain

  Python

  •77 forks•22 stars•55 issues•33 pull requests•Updated Apr 20, 2026Apr 20, 2026

• mpox

  Public
  Nextstrain build for mpox virus

  metadatabioinformaticspipeline+ 10

  metadatabioinformaticspipelinepathogenphylogeneticsgenbankaugurnextstrainauspicevirus-evolution+ 3

  Python

  •

  MIT License

  •2222 forks•5050 stars•1717 issues•88 pull requests•Updated Apr 20, 2026Apr 20, 2026

• lassa

  Public
  Nextstrain build for Lassa virus

  pathogennextstrain

  pathogennextstrain

  Python

  •55 forks•44 stars•99 issues•22 pull requests•Updated Apr 20, 2026Apr 20, 2026

• hmpv

  Public
  Human metapneumovirus pathogen build

  pathogennextstrain

  pathogennextstrain

  Python

  •00 forks•00 stars•55 issues•00 pull requests•Updated Apr 20, 2026Apr 20, 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 20, 2026Apr 20, 2026

• ebola

  Public
  Nextstrain build for Ebola virus

  pathogennextstrain

  pathogennextstrain

  Python

  •99 forks•44 stars•88 issues•11 pull request•Updated Apr 20, 2026Apr 20, 2026

• dengue

  Public
  Nextstrain build for dengue virus

  pathogennextstrain

  pathogennextstrain

  Python

  •1212 forks•1414 stars•1717 issues•11 pull request•Updated Apr 20, 2026Apr 20, 2026

• chikv

  Public
  Chikungunya virus workflows

  pathogennextstrain

  pathogennextstrain

  Python

  •00 forks•11 star•00 issues•00 pull requests•Updated Apr 20, 2026Apr 20, 2026

• avian-flu

  Public
  Nextstrain build for avian influenza viruses

  pathogennextstrain

  pathogennextstrain

  Python

  •1010 forks•2727 stars•1818 issues•66 pull requests•Updated Apr 20, 2026Apr 20, 2026