Repositories list

• augur

  Public
  Pipeline components for real-time phylodynamic analysis

  Python

  •

  GNU Affero General Public License v3.0

  •128•270•240•54•Updated Dec 23, 2024Dec 23, 2024

• auspice

  Public
  Web app for visualizing pathogen evolution

  JavaScript

  •

  GNU Affero General Public License v3.0

  •162•296•238•33•Updated Dec 21, 2024Dec 21, 2024

• WNV

  Public
  the repository used to build West Nile Virus for nextstrain

  pathogennextstrain

  Python

  •0•3•8•1•Updated Dec 20, 2024Dec 20, 2024

• dengue

  Public
  Nextstrain build for dengue virus

  pathogennextstrain

  Python

  •11•8•13•1•Updated Dec 20, 2024Dec 20, 2024

• yellow-fever

  Public
  pathogennextstrain

  Python

  •4•0•2•2•Updated Dec 20, 2024Dec 20, 2024

• hmpv

  Public
  Human metapneumovirus pathogen build

  pathogennextstrain

  Python

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

• oropouche

  Public
  Oropouche Nextstrain build

  pathogennextstrain

  Python

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

• mpox

  Public
  Nextstrain build for mpox virus

  metadatabioinformaticspipeline+ 10pathogenphylogeneticsgenbankaugurnextstrainauspicevirus-evolution+ 3

  Python

  •

  MIT License

  •19•45•27•7•Updated Dec 20, 2024Dec 20, 2024

• 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 Dec 20, 2024Dec 20, 2024

• fauna

  Public
  RethinkDB database to support real-time virus analysis

  Python

  •

  GNU Affero General Public License v3.0

  •13•33•20•12•Updated Dec 20, 2024Dec 20, 2024

• ncov

  Public
  Nextstrain build for novel coronavirus SARS-CoV-2

  pathogennextstrainncov+ 1sars-cov-2

  Python

  •

  MIT License

  •403•1.4k•71•22•Updated Dec 20, 2024Dec 20, 2024

• 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 Dec 19, 2024Dec 19, 2024

• status

  Public
  Nextstrain status pages

  Go

  •0•1•2•1•Updated Dec 19, 2024Dec 19, 2024

• nextstrain.org

  Public
  The Nextstrain website

  JavaScript

  •

  GNU Affero General Public License v3.0

  •48•90•69•11•Updated Dec 19, 2024Dec 19, 2024

• forecasts-ncov

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

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

  Python

  •2•7•11•7•Updated Dec 18, 2024Dec 18, 2024

• 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 Dec 18, 2024Dec 18, 2024

• docs.nextstrain.org

  Public
  Umbrella documentation project for Nextstrain

  Python

  •13•18•22•5•Updated Dec 18, 2024Dec 18, 2024

• steampipe-plugin-github

  Public
  Go

  •

  Apache License 2.0

  •31•0•0•0•Updated Dec 18, 2024Dec 18, 2024

• .github

  Public
  Shell

  •11•8•8•0•Updated Dec 18, 2024Dec 18, 2024

• seasonal-cov

  Public
  Nextstrain build for seasonal coronaviruses

  pathogennextstrain

  Python

  •0•1•4•1•Updated Dec 18, 2024Dec 18, 2024

• avian-flu

  Public
  Nextstrain build for avian influenza viruses

  pathogennextstrain

  Python

  •8•22•11•8•Updated Dec 17, 2024Dec 17, 2024

• zika

  Public
  Nextstrain build for Zika virus

  pathogennextstrain

  Python

  •11•8•4•1•Updated Dec 17, 2024Dec 17, 2024

• infra

  Public
  Nextstrain shared infrastructure

  Makefile

  •0•0•2•0•Updated Dec 17, 2024Dec 17, 2024

• seasonal-flu

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

  pathogennextstrain

  Python

  •27•46•23•0•Updated Dec 17, 2024Dec 17, 2024

• pathogen-repo-guide

  Public template
  Python

  •1•4•18•0•Updated Dec 16, 2024Dec 16, 2024

• nextclade_data

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

  Python

  •28•32•8•13•Updated Dec 16, 2024Dec 16, 2024

• nextclade

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

  scienceresearchvirus+ 17sequencingnext-generation-sequencingdnarnainfluenzasequencesstrain+ 10

  Rust

  •

  MIT License

  •61•220•111•19•Updated Dec 16, 2024Dec 16, 2024

• measles

  Public
  Nextstrain build for measles virus

  pathogennextstrain

  Python

  •6•1•5•5•Updated Dec 13, 2024Dec 13, 2024

• rubella

  Public
  Python

  •1•0•2•0•Updated Dec 11, 2024Dec 11, 2024

• public

  Public
  repo to house broad planning issues and other cross-repo concerns; see also https://github.com/nextstrain/private

  Shell

  •0•0•10•0•Updated Dec 10, 2024Dec 10, 2024