Repositories list

• rsv

  Public
  Workflow for RSV analyses on Nextstrain.org

  pathogennextstrain

  pathogennextstrain

  Python

  •8•11•8•4•Updated Mar 7, 2026Mar 7, 2026

• nextstrain.org

  Public
  The Nextstrain website

  JavaScript

  •

  GNU Affero General Public License v3.0

  •54•96•71•13•Updated Mar 6, 2026Mar 6, 2026

• nextclade_data

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

  Python

  •42•44•9•17•Updated Mar 6, 2026Mar 6, 2026

• measles

  Public
  Nextstrain build for measles virus

  pathogennextstrain

  pathogennextstrain

  Python

  •9•3•5•6•Updated Mar 6, 2026Mar 6, 2026

• vzv

  Public
  Pathogen workflow for varicella zoster virus

  Python

  •0•0•0•0•Updated Mar 6, 2026Mar 6, 2026

• WNV

  Public
  the repository used to build West Nile Virus for nextstrain

  pathogennextstrain

  pathogennextstrain

  Python

  •3•5•8•2•Updated Mar 6, 2026Mar 6, 2026

• mpox

  Public
  Nextstrain build for mpox virus

  metadatabioinformaticspipeline+ 10

  metadatabioinformaticspipelinepathogenphylogeneticsgenbankaugurnextstrainauspicevirus-evolution+ 3

  Python

  •

  MIT License

  •22•50•17•8•Updated Mar 6, 2026Mar 6, 2026

• dengue

  Public
  Nextstrain build for dengue virus

  pathogennextstrain

  pathogennextstrain

  Python

  •12•13•17•1•Updated Mar 6, 2026Mar 6, 2026

• mumps

  Public
  Nextstrain build for mumps virus

  pathogennextstrain

  pathogennextstrain

  Python

  •7•2•5•3•Updated Mar 6, 2026Mar 6, 2026

• ebola

  Public
  Nextstrain build for Ebola virus

  pathogennextstrain

  pathogennextstrain

  Python

  •9•4•7•1•Updated Mar 6, 2026Mar 6, 2026

• seasonal-flu

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

  pathogennextstrain

  pathogennextstrain

  Python

  •29•58•31•9•Updated Mar 6, 2026Mar 6, 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

  •21•37•33•9•Updated Mar 5, 2026Mar 5, 2026

• nextclade

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

  scienceresearchvirus+ 17

  scienceresearchvirussequencingnext-generation-sequencingdnarnainfluenzasequencesstrain+ 10

  TypeScript

  •

  MIT License

  •66•252•123•30•Updated Mar 5, 2026Mar 5, 2026

• rubella

  Public
  Nextstrain build for rubella virus

  pathogennextstrain

  pathogennextstrain

  Python

  •2•2•3•2•Updated Mar 5, 2026Mar 5, 2026

• hmpv

  Public
  Human metapneumovirus pathogen build

  pathogennextstrain

  pathogennextstrain

  Python

  •0•0•5•0•Updated Mar 5, 2026Mar 5, 2026

• augur

  Public
  Pipeline components for real-time phylodynamic analysis

  Python

  •

  GNU Affero General Public License v3.0

  •136•275•234•39•Updated Mar 5, 2026Mar 5, 2026

• variant-nowcast-hub

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

  R

  •

  MIT License

  •16•0•0•0•Updated Mar 4, 2026Mar 4, 2026

• bioconda-recipes

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

  Shell

  •3.8k•0•3•0•Updated Mar 4, 2026Mar 4, 2026

• docs.nextstrain.org

  Public
  Umbrella documentation project for Nextstrain

  Python

  •13•18•24•4•Updated Mar 4, 2026Mar 4, 2026

• conda-base

  Public
  Conda package build for nextstrain-base

  condamambanextstrain

  condamambanextstrain

  Shell

  •1•1•5•1•Updated Mar 4, 2026Mar 4, 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

  •20•28•70•4•Updated Mar 4, 2026Mar 4, 2026

• forecasts-ncov

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

  bioinformaticspathogenforecasts+ 4

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

  Python

  •3•9•12•3•Updated Mar 4, 2026Mar 4, 2026

• .github

  Public
  Shell

  •11•9•11•0•Updated Mar 4, 2026Mar 4, 2026

• docker-base

  Public
  Docker image build for nextstrain/base

  Shell

  •7•12•7•1•Updated Mar 4, 2026Mar 4, 2026

• sphinx-theme

  Public
  A Sphinx theme for Nextstrain's documentation, based on Read The Docs' default theme.

  HTML

  •

  MIT License

  •5•0•5•1•Updated Mar 4, 2026Mar 4, 2026

• ncov

  Public
  Nextstrain build for SARS-CoV-2

  pathogennextstrainncov+ 1

  pathogennextstrainncovsars-cov-2

  Python

  •

  MIT License

  •409•1.4k•74•22•Updated Mar 2, 2026Mar 2, 2026

• forecasts-flu

  Public
  Seasonal influenza variant growth rates and frequency forecasts

  pathogennextstrain

  pathogennextstrain

  Python

  •

  MIT License

  •0•1•10•1•Updated Feb 19, 2026Feb 19, 2026

• fauna

  Public
  RethinkDB database to support real-time virus analysis

  Python

  •

  GNU Affero General Public License v3.0

  •12•35•18•11•Updated Feb 19, 2026Feb 19, 2026

• yellow-fever

  Public
  pathogennextstrain

  pathogennextstrain

  Python

  •4•2•0•0•Updated Feb 13, 2026Feb 13, 2026

• avian-flu

  Public
  Nextstrain build for avian influenza viruses

  pathogennextstrain

  pathogennextstrain

  Python

  •10•27•18•6•Updated Feb 13, 2026Feb 13, 2026