Repositories list

• 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•7070 issues•33 pull requests•Updated Jun 15, 2026Jun 15, 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

  •2020 forks•3737 stars•3232 issues•1111 pull requests•Updated Jun 15, 2026Jun 15, 2026

• measles

  Public
  Nextstrain build for measles virus

  pathogennextstrain

  pathogennextstrain

  Python

  •99 forks•44 stars•77 issues•77 pull requests•Updated Jun 15, 2026Jun 15, 2026

• augur

  Public
  Pipeline components for real-time phylodynamic analysis

  Python

  •

  GNU Affero General Public License v3.0

  •136136 forks•277277 stars•230230 issues•3636 pull requests•Updated Jun 12, 2026Jun 12, 2026

• infra

  Public
  Nextstrain shared infrastructure

  Makefile

  •00 forks•00 stars•22 issues•22 pull requests•Updated Jun 12, 2026Jun 12, 2026

• seasonal-flu

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

  pathogennextstrain

  pathogennextstrain

  Python

  •3131 forks•6262 stars•2626 issues•77 pull requests•Updated Jun 12, 2026Jun 12, 2026

• avian-flu

  Public
  Nextstrain build for avian influenza viruses

  pathogennextstrain

  pathogennextstrain

  Python

  •1010 forks•2828 stars•1818 issues•66 pull requests•Updated Jun 12, 2026Jun 12, 2026

• bioconda-recipes

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

  Shell

  •4k4k forks•00 stars•33 issues•00 pull requests•Updated Jun 12, 2026Jun 12, 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 Jun 12, 2026Jun 12, 2026

• auspice.us

  Public
  JavaScript

  •88 forks•1313 stars•77 issues•33 pull requests•Updated Jun 11, 2026Jun 11, 2026

• auspice

  Public
  Web app for visualizing pathogen evolution

  JavaScript

  •

  GNU Affero General Public License v3.0

  •172172 forks•311311 stars•252252 issues•4444 pull requests•Updated Jun 11, 2026Jun 11, 2026

• nextstrain.org

  Public
  The Nextstrain website

  JavaScript

  •

  GNU Affero General Public License v3.0

  •5454 forks•9696 stars•6969 issues•1313 pull requests•Updated Jun 11, 2026Jun 11, 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 Jun 10, 2026Jun 10, 2026

• nextclade_data

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

  Python

  •4343 forks•4646 stars•1010 issues•1919 pull requests•Updated Jun 10, 2026Jun 10, 2026

• chikv

  Public
  Chikungunya virus workflows

  pathogennextstrain

  pathogennextstrain

  Python

  •00 forks•11 star•00 issues•00 pull requests•Updated Jun 9, 2026Jun 9, 2026

• oropouche

  Public
  Oropouche Nextstrain build

  pathogennextstrain

  pathogennextstrain

  Python

  •22 forks•11 star•00 issues•00 pull requests•Updated Jun 9, 2026Jun 9, 2026

• hmpv

  Public
  Human metapneumovirus pathogen build

  pathogennextstrain

  pathogennextstrain

  Python

  •00 forks•00 stars•55 issues•00 pull requests•Updated Jun 9, 2026Jun 9, 2026

• WNV

  Public
  the repository used to build West Nile Virus for nextstrain

  pathogennextstrain

  pathogennextstrain

  Python

  •33 forks•55 stars•77 issues•11 pull request•Updated Jun 9, 2026Jun 9, 2026

• lassa

  Public
  Nextstrain build for Lassa virus

  pathogennextstrain

  pathogennextstrain

  Python

  •55 forks•44 stars•99 issues•22 pull requests•Updated Jun 9, 2026Jun 9, 2026

• nipah

  Public
  pathogennextstrain

  pathogennextstrain

  Python

  •00 forks•22 stars•22 issues•00 pull requests•Updated Jun 9, 2026Jun 9, 2026

• rabies

  Public
  pathogennextstrain

  pathogennextstrain

  Python

  •22 forks•11 star•55 issues•00 pull requests•Updated Jun 9, 2026Jun 9, 2026

• ebola

  Public
  Nextstrain build for Ebola virus

  pathogennextstrain

  pathogennextstrain

  Python

  •1010 forks•55 stars•99 issues•11 pull request•Updated Jun 9, 2026Jun 9, 2026

• pathogen-repo-guide

  Public template
  Python

  •11 fork•44 stars•2323 issues•00 pull requests•Updated Jun 9, 2026Jun 9, 2026

• dengue

  Public
  Nextstrain build for dengue virus

  pathogennextstrain

  pathogennextstrain

  Python

  •1212 forks•1414 stars•1818 issues•11 pull request•Updated Jun 9, 2026Jun 9, 2026

• yellow-fever

  Public
  pathogennextstrain

  pathogennextstrain

  Python

  •55 forks•22 stars•11 issue•00 pull requests•Updated Jun 9, 2026Jun 9, 2026

• mumps

  Public
  Nextstrain build for mumps virus

  pathogennextstrain

  pathogennextstrain

  Python

  •77 forks•22 stars•55 issues•33 pull requests•Updated Jun 9, 2026Jun 9, 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 Jun 9, 2026Jun 9, 2026

• norovirus

  Public
  pathogennextstrain

  pathogennextstrain

  Python

  •

  MIT License

  •11 fork•33 stars•99 issues•11 pull request•Updated Jun 9, 2026Jun 9, 2026

• rubella

  Public
  Nextstrain build for rubella virus

  pathogennextstrain

  pathogennextstrain

  Python

  •22 forks•22 stars•33 issues•22 pull requests•Updated Jun 9, 2026Jun 9, 2026

• zika

  Public
  Nextstrain build for Zika virus

  pathogennextstrain

  pathogennextstrain

  Python

  •1111 forks•1010 stars•55 issues•22 pull requests•Updated Jun 9, 2026Jun 9, 2026