Repositories list

• seasonal-flu

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

  pathogennextstrain

  Python

  •29•57•31•10•Updated Jan 24, 2026Jan 24, 2026

• augur

  Public
  Pipeline components for real-time phylodynamic analysis

  Python

  •

  GNU Affero General Public License v3.0

  •136•275•234•40•Updated Jan 24, 2026Jan 24, 2026

• nextstrain.org

  Public
  The Nextstrain website

  JavaScript

  •

  GNU Affero General Public License v3.0

  •53•95•74•14•Updated Jan 23, 2026Jan 23, 2026

• chikv

  Public
  Chikungunya virus workflows

  pathogennextstrain

  Python

  •0•1•0•1•Updated Jan 23, 2026Jan 23, 2026

• measles

  Public
  Nextstrain build for measles virus

  pathogennextstrain

  Python

  •8•3•6•9•Updated Jan 23, 2026Jan 23, 2026

• bioconda-recipes

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

  Shell

  •3.7k•0•3•0•Updated Jan 22, 2026Jan 22, 2026

• ncov

  Public
  Nextstrain build for SARS-CoV-2

  pathogennextstrainncov+ 1sars-cov-2

  Python

  •

  MIT License

  •409•1.4k•74•23•Updated Jan 22, 2026Jan 22, 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 Jan 22, 2026Jan 22, 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

• 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 Jan 21, 2026Jan 21, 2026

• 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•29•Updated Jan 20, 2026Jan 20, 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 Nextstrain components like Augur and Auspice across computing environments such as Docker, Conda, and AWS Batch.

  Python

  •

  MIT License

  •20•28•67•4•Updated Jan 20, 2026Jan 20, 2026

• nextclade_data

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

  Python

  •41•43•9•17•Updated Jan 19, 2026Jan 19, 2026

• tb

  Public
  Nextstrain build for tuberculosis

  pathogennextstrain

  Python

  •10•4•11•1•Updated Jan 15, 2026Jan 15, 2026

• forecasts-flu

  Public
  Seasonal influenza variant growth rates and frequency forecasts

  pathogennextstrain

  Python

  •

  MIT License

  •0•1•8•1•Updated Jan 14, 2026Jan 14, 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

• rsv

  Public
  Workflow for RSV analyses on Nextstrain.org

  pathogennextstrain

  Python

  •6•10•10•5•Updated Jan 10, 2026Jan 10, 2026

• docs.nextstrain.org

  Public
  Umbrella documentation project for Nextstrain

  Python

  •13•18•25•3•Updated Jan 9, 2026Jan 9, 2026

• docker-base

  Public
  Docker image build for nextstrain/base

  Shell

  •7•12•7•1•Updated Jan 7, 2026Jan 7, 2026

• .github

  Public
  Shell

  •11•9•11•0•Updated Jan 6, 2026Jan 6, 2026

• mpox

  Public
  Nextstrain build for mpox virus

  metadatabioinformaticspipeline+ 10pathogenphylogeneticsgenbankaugurnextstrainauspicevirus-evolution+ 3

  Python

  •

  MIT License

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

• avian-flu

  Public
  Nextstrain build for avian influenza viruses

  pathogennextstrain

  Python

  •10•27•16•7•Updated Jan 4, 2026Jan 4, 2026

• forecasts-viz

  Public
  JavaScript

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

• infra

  Public
  Nextstrain shared infrastructure

  Makefile

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