Repositories list

• .github

  Public
  Shell

  •11•9•10•0•Updated Nov 26, 2025Nov 26, 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 Nov 26, 2025Nov 26, 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 Nov 26, 2025Nov 26, 2025

• ebola

  Public
  Nextstrain build for Ebola virus

  Python

  •9•3•6•1•Updated Nov 26, 2025Nov 26, 2025

• conda-base

  Public
  Conda package build for nextstrain-base

  condamambanextstrain

  Shell

  •1•1•6•1•Updated Nov 26, 2025Nov 26, 2025

• mpox

  Public
  Nextstrain build for mpox virus

  metadatabioinformaticspipeline+ 10pathogenphylogeneticsgenbankaugurnextstrainauspicevirus-evolution+ 3

  Python

  •

  MIT License

  •23•50•16•8•Updated Nov 26, 2025Nov 26, 2025

• 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•5•Updated Nov 26, 2025Nov 26, 2025

• 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 Nov 26, 2025Nov 26, 2025

• augur

  Public
  Pipeline components for real-time phylodynamic analysis

  Python

  •

  GNU Affero General Public License v3.0

  •135•275•234•40•Updated Nov 26, 2025Nov 26, 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 26, 2025Nov 26, 2025

• auspice.us

  Public
  JavaScript

  •8•13•5•1•Updated Nov 26, 2025Nov 26, 2025

• seasonal-flu

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

  pathogennextstrain

  Python

  •28•53•28•6•Updated Nov 26, 2025Nov 26, 2025

• measles

  Public
  Nextstrain build for measles virus

  pathogennextstrain

  Python

  •8•3•4•9•Updated Nov 26, 2025Nov 26, 2025

• ncov

  Public
  Nextstrain build for SARS-CoV-2

  pathogennextstrainncov+ 1sars-cov-2

  Python

  •

  MIT License

  •407•1.4k•73•22•Updated Nov 26, 2025Nov 26, 2025

• nextstrain.org

  Public
  The Nextstrain website

  JavaScript

  •

  GNU Affero General Public License v3.0

  •53•97•79•17•Updated Nov 26, 2025Nov 26, 2025

• test-github-actions

  Public
  A repo for testing GitHub actions

  Shell

  •1•0•0•0•Updated Nov 26, 2025Nov 26, 2025

• nextclade_data

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

  Python

  •38•41•9•14•Updated Nov 25, 2025Nov 25, 2025

• zika

  Public
  Nextstrain build for Zika virus

  pathogennextstrain

  Python

  •11•9•6•3•Updated Nov 25, 2025Nov 25, 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•20•Updated Nov 24, 2025Nov 24, 2025

• chikv

  Public
  Chikungunya virus workflows

  pathogennextstrain

  Python

  •0•0•0•0•Updated Nov 24, 2025Nov 24, 2025

• forecasts-flu

  Public
  Seasonal influenza variant growth rates and frequency forecasts

  pathogennextstrain

  Python

  •

  MIT License

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

• conda

  Public
  Nextstrain environment for the Conda package manager

  Shell

  •5•2•2•1•Updated Nov 24, 2025Nov 24, 2025

• ncov-clades-schema

  Public
  Renders SVG schema of SARS-CoV-2 clade as defined by Nextstrain

  phylogeneticsnextstrainsars-cov-2+ 1clades

  JavaScript

  •9•16•5•6•Updated Nov 24, 2025Nov 24, 2025

• docker-base

  Public
  Docker image build for nextstrain/base

  Shell

  •7•12•8•3•Updated Nov 24, 2025Nov 24, 2025

• tb

  Public
  Nextstrain build for tuberculosis

  pathogennextstrain

  Python

  •10•3•9•2•Updated Nov 20, 2025Nov 20, 2025

• fauna

  Public
  RethinkDB database to support real-time virus analysis

  Python

  •

  GNU Affero General Public License v3.0

  •13•34•18•11•Updated Nov 20, 2025Nov 20, 2025

• dengue

  Public
  Nextstrain build for dengue virus

  pathogennextstrain

  Python

  •12•11•17•1•Updated Nov 19, 2025Nov 19, 2025

• bioconda-recipes

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

  Shell

  •3.7k•0•3•0•Updated Nov 19, 2025Nov 19, 2025

• variant-nowcast-hub

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

  R

  •

  MIT License

  •14•0•0•0•Updated Nov 19, 2025Nov 19, 2025

• auspice

  Public
  Web app for visualizing pathogen evolution

  JavaScript

  •

  GNU Affero General Public License v3.0

  •168•305•252•40•Updated Nov 19, 2025Nov 19, 2025