Repositories list

• 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•27•62•6•Updated Mar 10, 2025Mar 10, 2025

• avian-flu

  Public
  Nextstrain build for avian influenza viruses

  pathogennextstrain

  Python

  •10•25•15•5•Updated Mar 10, 2025Mar 10, 2025

• nextclade

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

  scienceresearchvirus+ 17sequencingnext-generation-sequencingdnarnainfluenzasequencesstrain+ 10

  Rust

  •

  MIT License

  •60•226•111•23•Updated Mar 10, 2025Mar 10, 2025

• forecasts-viz

  Public
  JavaScript

  •0•1•2•1•Updated Mar 10, 2025Mar 10, 2025

• seasonal-flu

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

  pathogennextstrain

  Python

  •28•47•28•1•Updated Mar 8, 2025Mar 8, 2025

• dengue

  Public
  Nextstrain build for dengue virus

  pathogennextstrain

  Python

  •12•8•13•0•Updated Mar 7, 2025Mar 7, 2025

• WNV

  Public
  the repository used to build West Nile Virus for nextstrain

  pathogennextstrain

  Python

  •0•4•6•3•Updated Mar 7, 2025Mar 7, 2025

• nextstrain.org

  Public
  The Nextstrain website

  JavaScript

  •

  GNU Affero General Public License v3.0

  •50•95•69•12•Updated Mar 6, 2025Mar 6, 2025

• fauna

  Public
  RethinkDB database to support real-time virus analysis

  Python

  •

  GNU Affero General Public License v3.0

  •13•33•19•10•Updated Mar 6, 2025Mar 6, 2025

• lassa

  Public
  Nextstrain build for Lassa virus

  pathogennextstrain

  Python

  •5•0•8•0•Updated Mar 6, 2025Mar 6, 2025

• norovirus

  Public
  Python

  •

  MIT License

  •0•0•5•0•Updated Mar 5, 2025Mar 5, 2025

• nextclade_data

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

  Python

  •27•33•8•13•Updated Mar 5, 2025Mar 5, 2025

• ncov

  Public
  Nextstrain build for SARS-CoV-2

  pathogennextstrainncov+ 1sars-cov-2

  Python

  •

  MIT License

  •406•1.4k•72•22•Updated Mar 5, 2025Mar 5, 2025

• augur

  Public
  Pipeline components for real-time phylodynamic analysis

  Python

  •

  GNU Affero General Public License v3.0

  •130•268•219•35•Updated Mar 4, 2025Mar 4, 2025

• docs.nextstrain.org

  Public
  Umbrella documentation project for Nextstrain

  Python

  •13•18•22•5•Updated Mar 4, 2025Mar 4, 2025

• mpox

  Public
  Nextstrain build for mpox virus

  metadatabioinformaticspipeline+ 10pathogenphylogeneticsgenbankaugurnextstrainauspicevirus-evolution+ 3

  Python

  •

  MIT License

  •20•45•26•4•Updated Mar 4, 2025Mar 4, 2025

• zika

  Public
  Nextstrain build for Zika virus

  pathogennextstrain

  Python

  •10•8•3•2•Updated Mar 4, 2025Mar 4, 2025

• pathogen-repo-guide

  Public template
  Python

  •1•4•19•0•Updated Mar 4, 2025Mar 4, 2025

• docker-base

  Public
  Docker image build for nextstrain/base

  Shell

  •6•12•12•4•Updated Mar 4, 2025Mar 4, 2025

• ncov-clades-schema

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

  phylogeneticsnextstrainsars-cov-2+ 1clades

  JavaScript

  •8•14•4•4•Updated Mar 3, 2025Mar 3, 2025

• forecasts-ncov

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

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

  Python

  •2•7•11•5•Updated Mar 3, 2025Mar 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

  •20•36•30•8•Updated Mar 3, 2025Mar 3, 2025

• enterovirus_d68

  Public
  Enterovirus-D68 phylogenetic analyses code - actively maintained

  Python

  •5•1•2•0•Updated Mar 3, 2025Mar 3, 2025

• ingest

  Public
  Shared internal tooling for pathogen data ingest. Used by our pathogen build repos.

  Shell

  •0•1•2•0•Updated Feb 28, 2025Feb 28, 2025

• rsv

  Public
  Workflow for RSV analyses on Nextstrain.org

  pathogennextstrain

  Python

  •3•6•7•3•Updated Feb 28, 2025Feb 28, 2025

• auspice

  Public
  Web app for visualizing pathogen evolution

  JavaScript

  •

  GNU Affero General Public License v3.0

  •166•299•232•32•Updated Feb 25, 2025Feb 25, 2025

• bioconda-recipes

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

  Shell

  •3.4k•0•3•0•Updated Feb 25, 2025Feb 25, 2025

• ebola

  Public
  Nextstrain build for Ebola virus

  Python

  •9•3•4•3•Updated Feb 15, 2025Feb 15, 2025

• .github

  Public
  Shell

  •11•8•9•1•Updated Feb 14, 2025Feb 14, 2025

• flu_frequencies

  Public
  Flu clade and mutation frequencies

  mutationsinfluenzaflu+ 1clades

  TypeScript

  •3•3•7•4•Updated Feb 14, 2025Feb 14, 2025