Repositories list

• seasonal-flu

  Public

  nextstrain/seasonal-flu’s past year of commit activity
  Scripts. config, and snakefiles for seasonal-flu nextstrain builds

  pathogennextstrain

  Python

  •28•53•28•6•Updated Nov 16, 2025Nov 16, 2025

• nextclade_data

  Public

  nextstrain/nextclade_data’s past year of commit activity
  Datasets for https://github.com/nextstrain/nextclade

  Python

  •37•41•9•15•Updated Nov 14, 2025Nov 14, 2025

• mpox

  Public

  nextstrain/mpox’s past year of commit activity
  Nextstrain build for mpox virus

  metadatabioinformaticspipeline+ 10pathogenphylogeneticsgenbankaugurnextstrainauspicevirus-evolution+ 3

  Python

  •

  MIT License

  •23•50•16•8•Updated Nov 14, 2025Nov 14, 2025

• avian-flu

  Public

  nextstrain/avian-flu’s past year of commit activity
  Nextstrain build for avian influenza viruses

  pathogennextstrain

  Python

  •10•27•16•6•Updated Nov 14, 2025Nov 14, 2025

• nextstrain.org

  Public

  nextstrain/nextstrain.org’s past year of commit activity
  The Nextstrain website

  JavaScript

  •

  GNU Affero General Public License v3.0

  •53•97•80•15•Updated Nov 13, 2025Nov 13, 2025

• fauna

  Public

  nextstrain/fauna’s past year of commit activity
  RethinkDB database to support real-time virus analysis

  Python

  •

  GNU Affero General Public License v3.0

  •13•34•18•11•Updated Nov 13, 2025Nov 13, 2025

• variant-nowcast-hub

  Public

  nextstrain/variant-nowcast-hub’s past year of commit activity
  A repository to store COVID-19 variant nowcasts collected as a modeling hub.

  R

  •

  MIT License

  •14•0•0•0•Updated Nov 12, 2025Nov 12, 2025

• norovirus

  Public
  pathogennextstrain

  Python

  •

  MIT License

  •1•2•6•1•Updated Nov 10, 2025Nov 10, 2025

• .github

  Public

  nextstrain/.github’s past year of commit activity
  Shell

  •11•9•10•1•Updated Nov 10, 2025Nov 10, 2025

• tb

  Public

  nextstrain/tb’s past year of commit activity
  Nextstrain build for tuberculosis

  pathogennextstrain

  Python

  •10•3•10•2•Updated Nov 10, 2025Nov 10, 2025

• rsv

  Public

  nextstrain/rsv’s past year of commit activity
  Workflow for RSV analyses on Nextstrain.org

  pathogennextstrain

  Python

  •6•10•11•7•Updated Nov 9, 2025Nov 9, 2025

• auspice

  Public

  nextstrain/auspice’s past year of commit activity
  Web app for visualizing pathogen evolution

  JavaScript

  •

  GNU Affero General Public License v3.0

  •168•304•251•39•Updated Nov 7, 2025Nov 7, 2025

• cli

  Public

  nextstrain/cli’s past year of commit activity
  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•5•Updated Nov 7, 2025Nov 7, 2025

• docker-base

  Public
  Docker image build for nextstrain/base

  Shell

  •7•12•8•2•Updated Nov 6, 2025Nov 6, 2025

• chikv

  Public

  nextstrain/chikv’s past year of commit activity
  Chikungunya virus workflows

  pathogennextstrain

  Python

  •0•0•1•0•Updated Nov 6, 2025Nov 6, 2025

• mumps

  Public

  nextstrain/mumps’s past year of commit activity
  Nextstrain build for mumps virus

  pathogennextstrain

  Python

  •7•2•5•3•Updated Nov 5, 2025Nov 5, 2025

• augur

  Public

  nextstrain/augur’s past year of commit activity
  Pipeline components for real-time phylodynamic analysis

  Python

  •

  GNU Affero General Public License v3.0

  •136•275•235•41•Updated Nov 4, 2025Nov 4, 2025

• pathogen-repo-guide

  Public template

  nextstrain/pathogen-repo-guide’s past year of commit activity
  Python

  •1•4•22•0•Updated Nov 4, 2025Nov 4, 2025

• forecasts-ncov

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

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

  Python

  •3•8•12•3•Updated Nov 3, 2025Nov 3, 2025

• nextclade

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

  scienceresearchvirus+ 17sequencingnext-generation-sequencingdnarnainfluenzasequencesstrain+ 10

  TypeScript

  •

  MIT License

  •66•247•119•19•Updated Nov 3, 2025Nov 3, 2025

• yellow-fever

  Public

  nextstrain/yellow-fever’s past year of commit activity
  pathogennextstrain

  Python

  •4•1•0•0•Updated Nov 3, 2025Nov 3, 2025

• auspice.us

  Public

  nextstrain/auspice.us’s past year of commit activity
  JavaScript

  •8•13•4•1•Updated Nov 3, 2025Nov 3, 2025

• 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+ 5genbanknextstrainncovsars-cov-2gisaid

  Python

  •

  MIT License

  •19•37•32•8•Updated Oct 31, 2025Oct 31, 2025

• hmpv

  Public
  Human metapneumovirus pathogen build

  pathogennextstrain

  Python

  •0•0•6•0•Updated Oct 30, 2025Oct 30, 2025

• measles

  Public
  Nextstrain build for measles virus

  pathogennextstrain

  Python

  •8•3•4•9•Updated Oct 29, 2025Oct 29, 2025

• infra

  Public

  nextstrain/infra’s past year of commit activity
  Nextstrain shared infrastructure

  Makefile

  •0•0•2•0•Updated Oct 29, 2025Oct 29, 2025

• sphinx-theme

  Public

  nextstrain/sphinx-theme’s past year of commit activity
  A Sphinx theme for Nextstrain's documentation, based on Read The Docs' default theme.

  HTML

  •

  MIT License

  •5•0•5•1•Updated Oct 29, 2025Oct 29, 2025

• conda-base

  Public

  nextstrain/conda-base’s past year of commit activity
  Conda package build for nextstrain-base

  condamambanextstrain

  Shell

  •1•1•6•1•Updated Oct 29, 2025Oct 29, 2025

• shared

  Public
  Shared internal tooling for pathogen workflows. Used by our individual pathogen repos which produce Nextstrain builds.

  Python

  •1•1•5•4•Updated Oct 28, 2025Oct 28, 2025

• forecasts-flu

  Public
  Seasonal influenza variant growth rates and frequency forecasts

  pathogennextstrain

  Python

  •

  MIT License

  •0•1•2•1•Updated Oct 24, 2025Oct 24, 2025