Repositories list

• seasonal-flu

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

  pathogennextstrain

  Python

  •29•57•31•10•Updated Feb 9, 2026Feb 9, 2026

• .github

  Public
  Shell

  •11•9•11•1•Updated Feb 9, 2026Feb 9, 2026

• docker-base

  Public
  Docker image build for nextstrain/base

  Shell

  •7•12•7•2•Updated Feb 9, 2026Feb 9, 2026

• augur

  Public
  Pipeline components for real-time phylodynamic analysis

  Python

  •

  GNU Affero General Public License v3.0

  •136•275•233•39•Updated Feb 9, 2026Feb 9, 2026

• nextstrain.org

  Public
  The Nextstrain website

  JavaScript

  •

  GNU Affero General Public License v3.0

  •53•96•74•13•Updated Feb 6, 2026Feb 6, 2026

• forecasts-flu

  Public
  Seasonal influenza variant growth rates and frequency forecasts

  pathogennextstrain

  Python

  •

  MIT License

  •0•1•9•2•Updated Feb 6, 2026Feb 6, 2026

• forecasts-viz

  Public
  JavaScript

  •0•2•6•5•Updated Feb 6, 2026Feb 6, 2026

• docs.nextstrain.org

  Public
  Umbrella documentation project for Nextstrain

  Python

  •13•18•25•5•Updated Feb 6, 2026Feb 6, 2026

• bioconda-recipes

  Public

  nextstrain/bioconda-recipes’s past year of commit activity
  Fork for maintaining Nextstrain-related recipes and submitting PRs upstream.

  Shell

  •3.7k•0•3•0•Updated Feb 5, 2026Feb 5, 2026

• mpox

  Public
  Nextstrain build for mpox virus

  metadatabioinformaticspipeline+ 10pathogenphylogeneticsgenbankaugurnextstrainauspicevirus-evolution+ 3

  Python

  •

  MIT License

  •23•50•17•8•Updated Feb 5, 2026Feb 5, 2026

• nextclade

  Public

  nextstrain/nextclade’s past year of commit activity
  Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement

  scienceresearchvirus+ 17sequencingnext-generation-sequencingdnarnainfluenzasequencesstrain+ 10

  TypeScript

  •

  MIT License

  •66•250•122•29•Updated Feb 5, 2026Feb 5, 2026

• tb

  Public
  Nextstrain build for tuberculosis

  pathogennextstrain

  Python

  •10•4•9•1•Updated Feb 5, 2026Feb 5, 2026

• measles

  Public
  Nextstrain build for measles virus

  pathogennextstrain

  Python

  •7•3•7•9•Updated Feb 4, 2026Feb 4, 2026

• rsv

  Public
  Workflow for RSV analyses on Nextstrain.org

  pathogennextstrain

  Python

  •7•10•9•6•Updated Feb 4, 2026Feb 4, 2026

• shared

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

  Python

  •1•1•6•2•Updated Feb 4, 2026Feb 4, 2026

• avian-flu

  Public
  Nextstrain build for avian influenza viruses

  pathogennextstrain

  Python

  •10•27•18•6•Updated Feb 4, 2026Feb 4, 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+ 5genbanknextstrainncovsars-cov-2gisaid

  Python

  •

  MIT License

  •20•37•33•9•Updated Feb 4, 2026Feb 4, 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 Feb 4, 2026Feb 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•5•Updated Feb 3, 2026Feb 3, 2026

• ncov

  Public
  Nextstrain build for SARS-CoV-2

  pathogennextstrainncov+ 1sars-cov-2

  Python

  •

  MIT License

  •409•1.4k•74•22•Updated Jan 31, 2026Jan 31, 2026

• WNV

  Public
  the repository used to build West Nile Virus for nextstrain

  pathogennextstrain

  Python

  •2•5•7•2•Updated Jan 30, 2026Jan 30, 2026

• chikv

  Public
  Chikungunya virus workflows

  pathogennextstrain

  Python

  •0•1•0•0•Updated Jan 27, 2026Jan 27, 2026

• nextclade_data

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

  Python

  •42•43•9•17•Updated Jan 26, 2026Jan 26, 2026

• fauna

  Public
  RethinkDB database to support real-time virus analysis

  Python

  •

  GNU Affero General Public License v3.0

  •13•35•18•11•Updated Jan 21, 2026Jan 21, 2026

• auspice

  Public
  Web app for visualizing pathogen evolution

  JavaScript

  •

  GNU Affero General Public License v3.0

  •168•305•252•36•Updated Jan 21, 2026Jan 21, 2026

• 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 Jan 12, 2026Jan 12, 2026

• norovirus

  Public
  pathogennextstrain

  Python

  •

  MIT License

  •1•2•8•1•Updated Jan 5, 2026Jan 5, 2026

• ebola

  Public
  Nextstrain build for Ebola virus

  pathogennextstrain

  Python

  •9•4•7•1•Updated Jan 5, 2026Jan 5, 2026

• conda-base

  Public
  Conda package build for nextstrain-base

  condamambanextstrain

  Shell

  •1•1•5•1•Updated Jan 5, 2026Jan 5, 2026

• infra

  Public
  Nextstrain shared infrastructure

  Makefile

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