Repositories list

• rsv

  Public
  Workflow for RSV analyses on Nextstrain.org

  pathogennextstrain

  pathogennextstrain

  Python

  •66 forks•1111 stars•99 issues•44 pull requests•Updated May 30, 2026May 30, 2026

• infra

  Public
  Nextstrain shared infrastructure

  Makefile

  •00 forks•00 stars•22 issues•00 pull requests•Updated May 29, 2026May 29, 2026

• augur

  Public
  Pipeline components for real-time phylodynamic analysis

  Python

  •

  GNU Affero General Public License v3.0

  •136136 forks•275275 stars•229229 issues•3636 pull requests•Updated May 29, 2026May 29, 2026

• ebola

  Public
  Nextstrain build for Ebola virus

  pathogennextstrain

  pathogennextstrain

  Python

  •1010 forks•55 stars•99 issues•22 pull requests•Updated May 29, 2026May 29, 2026

• nextclade_data

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

  Python

  •4343 forks•4545 stars•1010 issues•1717 pull requests•Updated May 29, 2026May 29, 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 May 28, 2026May 28, 2026

• auspice

  Public
  Web app for visualizing pathogen evolution

  JavaScript

  •

  GNU Affero General Public License v3.0

  •171171 forks•311311 stars•253253 issues•4040 pull requests•Updated May 28, 2026May 28, 2026

• auspice.us

  Public
  JavaScript

  •88 forks•1313 stars•66 issues•22 pull requests•Updated May 28, 2026May 28, 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 May 27, 2026May 27, 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 May 27, 2026May 27, 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 May 26, 2026May 26, 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•258258 stars•118118 issues•3030 pull requests•Updated May 26, 2026May 26, 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•3333 issues•1010 pull requests•Updated May 25, 2026May 25, 2026

• tb

  Public
  Nextstrain build for tuberculosis

  pathogennextstrain

  pathogennextstrain

  Python

  •1010 forks•44 stars•1010 issues•11 pull request•Updated May 25, 2026May 25, 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 May 25, 2026May 25, 2026

• avian-flu

  Public
  Nextstrain build for avian influenza viruses

  pathogennextstrain

  pathogennextstrain

  Python

  •1010 forks•2828 stars•1818 issues•66 pull requests•Updated May 25, 2026May 25, 2026

• ncov

  Public
  Nextstrain build for SARS-CoV-2

  pathogennextstrainncov+ 1

  pathogennextstrainncovsars-cov-2

  Python

  •

  MIT License

  •408408 forks•1.4k1.4k stars•7474 issues•2323 pull requests•Updated May 25, 2026May 25, 2026

• forecasts-viz

  Public
  TypeScript

  •00 forks•22 stars•77 issues•11 pull request•Updated May 22, 2026May 22, 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•44 pull requests•Updated May 21, 2026May 21, 2026

• docs.nextstrain.org

  Public
  Umbrella documentation project for Nextstrain

  Python

  •1313 forks•1818 stars•2525 issues•44 pull requests•Updated May 20, 2026May 20, 2026

• .github

  Public
  Shell

  •1111 forks•99 stars•1212 issues•00 pull requests•Updated May 20, 2026May 20, 2026

• chikv

  Public
  Chikungunya virus workflows

  pathogennextstrain

  pathogennextstrain

  Python

  •00 forks•11 star•00 issues•00 pull requests•Updated May 19, 2026May 19, 2026

• seasonal-cov

  Public
  Nextstrain build for seasonal coronaviruses

  pathogennextstrain

  pathogennextstrain

  Python

  •00 forks•11 star•11 issue•00 pull requests•Updated May 19, 2026May 19, 2026

• rabies

  Public
  pathogennextstrain

  pathogennextstrain

  Python

  •22 forks•11 star•55 issues•00 pull requests•Updated May 19, 2026May 19, 2026

• norovirus

  Public
  pathogennextstrain

  pathogennextstrain

  Python

  •

  MIT License

  •11 fork•33 stars•99 issues•11 pull request•Updated May 19, 2026May 19, 2026

• andv

  Public
  Andes hantavirus

  Python

  •00 forks•00 stars•00 issues•22 pull requests•Updated May 12, 2026May 12, 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 May 11, 2026May 11, 2026

• forecasts-flu

  Public
  Seasonal influenza variant growth rates and frequency forecasts

  pathogennextstrain

  pathogennextstrain

  Python

  •

  MIT License

  •00 forks•11 star•1111 issues•11 pull request•Updated May 11, 2026May 11, 2026

• measles

  Public
  Nextstrain build for measles virus

  pathogennextstrain

  pathogennextstrain

  Python

  •99 forks•33 stars•77 issues•66 pull requests•Updated Apr 30, 2026Apr 30, 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