Repositories list

• augur

  Public
  Pipeline components for real-time phylodynamic analysis

  Python

  •

  GNU Affero General Public License v3.0

  •128•269•223•37•Updated Jan 29, 2025Jan 29, 2025

• ncov

  Public
  Nextstrain build for novel coronavirus SARS-CoV-2

  pathogennextstrainncov+ 1sars-cov-2

  Python

  •

  MIT License

  •403•1.4k•72•23•Updated Jan 28, 2025Jan 28, 2025

• nextclade_data

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

  Python

  •27•32•8•12•Updated Jan 28, 2025Jan 28, 2025

• WNV

  Public
  the repository used to build West Nile Virus for nextstrain

  pathogennextstrain

  Python

  •0•3•6•3•Updated Jan 28, 2025Jan 28, 2025

• tb

  Public
  Nextstrain build for tuberculosis

  Python

  •8•2•4•1•Updated Jan 28, 2025Jan 28, 2025

• nextclade

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

  scienceresearchvirus+ 17sequencingnext-generation-sequencingdnarnainfluenzasequencesstrain+ 10

  Rust

  •

  MIT License

  •61•224•112•20•Updated Jan 28, 2025Jan 28, 2025

• seasonal-flu

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

  pathogennextstrain

  Python

  •27•46•23•0•Updated Jan 27, 2025Jan 27, 2025

• mpox

  Public
  Nextstrain build for mpox virus

  metadatabioinformaticspipeline+ 10pathogenphylogeneticsgenbankaugurnextstrainauspicevirus-evolution+ 3

  Python

  •

  MIT License

  •20•45•26•4•Updated Jan 27, 2025Jan 27, 2025

• status

  Public
  Nextstrain status pages

  Go

  •

  MIT License

  •0•1•2•0•Updated Jan 27, 2025Jan 27, 2025

• fauna

  Public
  RethinkDB database to support real-time virus analysis

  Python

  •

  GNU Affero General Public License v3.0

  •13•33•19•10•Updated Jan 27, 2025Jan 27, 2025

• nextstrain.org

  Public
  The Nextstrain website

  JavaScript

  •

  GNU Affero General Public License v3.0

  •49•93•68•9•Updated Jan 24, 2025Jan 24, 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•31•8•Updated Jan 23, 2025Jan 23, 2025

• steampipe-plugin-github

  Public
  Go

  •

  Apache License 2.0

  •31•0•0•0•Updated Jan 23, 2025Jan 23, 2025

• avian-flu

  Public
  Nextstrain build for avian influenza viruses

  pathogennextstrain

  Python

  •9•22•11•8•Updated Jan 23, 2025Jan 23, 2025

• auspice

  Public
  Web app for visualizing pathogen evolution

  JavaScript

  •

  GNU Affero General Public License v3.0

  •163•296•232•29•Updated Jan 22, 2025Jan 22, 2025

• bioconda-recipes

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

  Shell

  •3.3k•0•3•0•Updated Jan 22, 2025Jan 22, 2025

• lassa

  Public
  Nextstrain build for Lassa virus

  pathogennextstrain

  Python

  •5•0•10•1•Updated Jan 22, 2025Jan 22, 2025

• auspice.us

  Public
  JavaScript

  •8•13•6•1•Updated Jan 22, 2025Jan 22, 2025

• rabies

  Public
  pathogennextstrain

  Python

  •0•0•5•0•Updated Jan 17, 2025Jan 17, 2025

• dengue

  Public
  Nextstrain build for dengue virus

  pathogennextstrain

  Python

  •12•8•13•0•Updated Jan 17, 2025Jan 17, 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•6•Updated Jan 17, 2025Jan 17, 2025

• forecasts-viz

  Public
  JavaScript

  •0•1•2•1•Updated Jan 17, 2025Jan 17, 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•27•61•3•Updated Jan 16, 2025Jan 16, 2025

• yellow-fever

  Public
  pathogennextstrain

  Python

  •4•0•0•0•Updated Jan 9, 2025Jan 9, 2025

• seasonal-cov

  Public
  Nextstrain build for seasonal coronaviruses

  pathogennextstrain

  Python

  •0•1•1•0•Updated Jan 9, 2025Jan 9, 2025

• hmpv

  Public
  Human metapneumovirus pathogen build

  pathogennextstrain

  Python

  •0•0•7•0•Updated Jan 8, 2025Jan 8, 2025

• docker-base

  Public
  Docker image build for nextstrain/base

  Shell

  •6•12•12•4•Updated Jan 7, 2025Jan 7, 2025

• conda-base

  Public
  Conda package build for nextstrain-base

  condamambanextstrain

  Shell

  •1•1•8•2•Updated Jan 7, 2025Jan 7, 2025

• ncov-clades-schema

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

  phylogeneticsnextstrainsars-cov-2+ 1clades

  JavaScript

  •8•11•4•3•Updated Dec 25, 2024Dec 25, 2024

• oropouche

  Public
  Oropouche Nextstrain build

  pathogennextstrain

  Python

  •0•1•0•0•Updated Dec 20, 2024Dec 20, 2024