Repositories list

• WNV

  Public
  the repository used to build West Nile Virus for nextstrain

  pathogennextstrain

  Python

  •0•2•8•2•Updated Nov 15, 2024Nov 15, 2024

• augur

  Public
  Pipeline components for real-time phylodynamic analysis

  Python

  •

  GNU Affero General Public License v3.0

  •128•268•241•54•Updated Nov 15, 2024Nov 15, 2024

• nextstrain.org

  Public
  The Nextstrain website

  JavaScript

  •

  GNU Affero General Public License v3.0

  •48•89•85•15•Updated Nov 15, 2024Nov 15, 2024

• auspice

  Public
  Web app for visualizing pathogen evolution

  JavaScript

  •

  GNU Affero General Public License v3.0

  •161•292•239•51•Updated Nov 15, 2024Nov 15, 2024

• avian-flu

  Public
  Nextstrain build for avian influenza viruses

  pathogennextstrain

  Python

  •7•20•11•3•Updated Nov 15, 2024Nov 15, 2024

• nextclade

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

  scienceresearchvirus+ 17sequencingnext-generation-sequencingdnarnainfluenzasequencesstrain+ 10

  Rust

  •

  MIT License

  •61•219•108•18•Updated Nov 14, 2024Nov 14, 2024

• auspice.us

  Public
  JavaScript

  •8•13•6•1•Updated Nov 14, 2024Nov 14, 2024

• mpox

  Public
  Nextstrain build for mpox virus

  metadatabioinformaticspipeline+ 10pathogenphylogeneticsgenbankaugurnextstrainauspicevirus-evolution+ 3

  Python

  •

  MIT License

  •19•45•25•7•Updated Nov 14, 2024Nov 14, 2024

• nextclade_data

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

  Python

  •28•32•8•14•Updated Nov 14, 2024Nov 14, 2024

• fauna

  Public
  RethinkDB database to support real-time virus analysis

  Python

  •

  GNU Affero General Public License v3.0

  •13•33•18•10•Updated Nov 14, 2024Nov 14, 2024

• ncov

  Public
  Nextstrain build for novel coronavirus SARS-CoV-2

  pathogennextstrainncov+ 1sars-cov-2

  Python

  •

  MIT License

  •403•1.4k•70•21•Updated Nov 14, 2024Nov 14, 2024

• human-metapneumovirus

  Public
  Human metapneumovirus pathogen build

  Python

  •0•0•0•0•Updated Nov 14, 2024Nov 14, 2024

• status

  Public
  Nextstrain status pages

  JavaScript

  •0•1•8•0•Updated Nov 13, 2024Nov 13, 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•30•9•Updated Nov 13, 2024Nov 13, 2024

• seasonal-flu

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

  pathogennextstrain

  Python

  •26•45•27•2•Updated Nov 13, 2024Nov 13, 2024

• nipah

  Public
  pathogennextstrain

  Python

  •0•0•1•0•Updated Nov 8, 2024Nov 8, 2024

• dengue

  Public
  Nextstrain build for dengue virus

  pathogennextstrain

  Python

  •11•8•10•0•Updated Nov 7, 2024Nov 7, 2024

• rabies

  Public
  pathogennextstrain

  Python

  •0•0•5•0•Updated Nov 7, 2024Nov 7, 2024

• measles

  Public
  Nextstrain build for measles virus

  pathogennextstrain

  Python

  •6•1•4•5•Updated Nov 6, 2024Nov 6, 2024

• public

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

  0•0•6•0•Updated Nov 6, 2024Nov 6, 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 Nov 5, 2024Nov 5, 2024

• oropouche

  Public
  Oropouche Nextstrain build

  pathogennextstrain

  Python

  •0•1•2•0•Updated Nov 5, 2024Nov 5, 2024

• norovirus

  Public
  Python

  •

  MIT License

  •0•0•4•0•Updated Nov 4, 2024Nov 4, 2024

• zika-tutorial

  Public
  Data and scripts for Zika virus tutorial

  Python

  •27•10•1•3•Updated Nov 4, 2024Nov 4, 2024

• rsv

  Public
  Workflow for RSV analyses on Nextstrain.org

  pathogennextstrain

  Python

  •3•6•5•3•Updated Oct 29, 2024Oct 29, 2024

• bioconda-recipes

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

  Shell

  •3.3k•0•3•0•Updated Oct 29, 2024Oct 29, 2024

• docker-base

  Public
  Docker image build for nextstrain/base

  Shell

  •6•12•12•4•Updated Oct 25, 2024Oct 25, 2024

• seasonal-cov

  Public
  Nextstrain build for seasonal coronaviruses

  pathogennextstrain

  Python

  •0•1•3•1•Updated Oct 25, 2024Oct 25, 2024

• infra

  Public
  Nextstrain shared infrastructure

  Makefile

  •0•0•2•0•Updated Oct 24, 2024Oct 24, 2024

• conda-base

  Public
  Conda package build for nextstrain-base

  condamambanextstrain

  Shell

  •1•1•8•2•Updated Oct 23, 2024Oct 23, 2024