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 Nextstrain components like Augur and Auspice across computing environments such as Docker, Conda, and AWS Batch.

  Python

  •

  MIT License

  •20•28•68•6•Updated Dec 31, 2025Dec 31, 2025

• nextclade_data

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

  Python

  •41•42•9•18•Updated Dec 29, 2025Dec 29, 2025

• measles

  Public
  Nextstrain build for measles virus

  pathogennextstrain

  Python

  •8•3•4•11•Updated Dec 26, 2025Dec 26, 2025

• variant-nowcast-hub

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

  R

  •

  MIT License

  •15•0•0•0•Updated Dec 24, 2025Dec 24, 2025

• forecasts-flu

  Public
  Seasonal influenza variant growth rates and frequency forecasts

  pathogennextstrain

  Python

  •

  MIT License

  •0•1•2•1•Updated Dec 23, 2025Dec 23, 2025

• ebola

  Public
  Nextstrain build for Ebola virus

  pathogennextstrain

  Python

  •9•4•6•2•Updated Dec 23, 2025Dec 23, 2025

• seasonal-flu

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

  pathogennextstrain

  Python

  •29•56•33•9•Updated Dec 23, 2025Dec 23, 2025

• forecasts-viz

  Public
  JavaScript

  •0•2•6•4•Updated Dec 23, 2025Dec 23, 2025

• mpox

  Public
  Nextstrain build for mpox virus

  metadatabioinformaticspipeline+ 10pathogenphylogeneticsgenbankaugurnextstrainauspicevirus-evolution+ 3

  Python

  •

  MIT License

  •23•50•16•8•Updated Dec 23, 2025Dec 23, 2025

• .github

  Public
  Shell

  •11•9•11•1•Updated Dec 23, 2025Dec 23, 2025

• ncov

  Public
  Nextstrain build for SARS-CoV-2

  pathogennextstrainncov+ 1sars-cov-2

  Python

  •

  MIT License

  •409•1.4k•75•22•Updated Dec 23, 2025Dec 23, 2025

• infra

  Public
  Nextstrain shared infrastructure

  Makefile

  •0•0•2•0•Updated Dec 22, 2025Dec 22, 2025

• norovirus

  Public
  pathogennextstrain

  Python

  •

  MIT License

  •1•2•7•2•Updated Dec 22, 2025Dec 22, 2025

• chikv

  Public
  Chikungunya virus workflows

  pathogennextstrain

  Python

  •0•1•0•0•Updated Dec 22, 2025Dec 22, 2025

• avian-flu

  Public
  Nextstrain build for avian influenza viruses

  pathogennextstrain

  Python

  •10•27•16•7•Updated Dec 21, 2025Dec 21, 2025

• nextstrain.org

  Public
  The Nextstrain website

  JavaScript

  •

  GNU Affero General Public License v3.0

  •53•96•78•21•Updated Dec 20, 2025Dec 20, 2025

• mumps

  Public
  Nextstrain build for mumps virus

  pathogennextstrain

  Python

  •7•2•5•3•Updated Dec 19, 2025Dec 19, 2025

• nipah

  Public
  pathogennextstrain

  Python

  •0•1•3•0•Updated Dec 19, 2025Dec 19, 2025

• oropouche

  Public
  Oropouche Nextstrain build

  pathogennextstrain

  Python

  •1•1•0•0•Updated Dec 19, 2025Dec 19, 2025

• rabies

  Public
  pathogennextstrain

  Python

  •1•0•4•0•Updated Dec 19, 2025Dec 19, 2025

• rubella

  Public
  Nextstrain build for rubella virus

  pathogennextstrain

  Python

  •2•2•3•2•Updated Dec 19, 2025Dec 19, 2025

• yellow-fever

  Public
  pathogennextstrain

  Python

  •4•2•0•0•Updated Dec 19, 2025Dec 19, 2025

• zika

  Public
  Nextstrain build for Zika virus

  pathogennextstrain

  Python

  •11•10•5•2•Updated Dec 19, 2025Dec 19, 2025

• fauna

  Public
  RethinkDB database to support real-time virus analysis

  Python

  •

  GNU Affero General Public License v3.0

  •13•34•18•11•Updated Dec 19, 2025Dec 19, 2025

• hmpv

  Public
  Human metapneumovirus pathogen build

  pathogennextstrain

  Python

  •0•0•5•0•Updated Dec 18, 2025Dec 18, 2025

• dengue

  Public
  Nextstrain build for dengue virus

  pathogennextstrain

  Python

  •12•12•16•1•Updated Dec 16, 2025Dec 16, 2025

• nextclade

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

  scienceresearchvirus+ 17sequencingnext-generation-sequencingdnarnainfluenzasequencesstrain+ 10

  TypeScript

  •

  MIT License

  •66•250•120•23•Updated Dec 15, 2025Dec 15, 2025

• conda-base

  Public
  Conda package build for nextstrain-base

  condamambanextstrain

  Shell

  •1•1•5•3•Updated Dec 15, 2025Dec 15, 2025

• augur

  Public
  Pipeline components for real-time phylodynamic analysis

  Python

  •

  GNU Affero General Public License v3.0

  •135•275•233•36•Updated Dec 15, 2025Dec 15, 2025

• forecasts-ncov

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

  bioinformaticspathogenforecasts+ 4nextstrainsars-cov-2pango-lineagessars-cov-2-variants

  Python

  •3•9•12•3•Updated Dec 15, 2025Dec 15, 2025