Repositories list

• nextclade_data

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

  Python

  •28•32•8•13•Updated Nov 27, 2024Nov 27, 2024

• yellow-fever

  Public
  pathogennextstrain

  Python

  •4•0•2•0•Updated Nov 27, 2024Nov 27, 2024

• docs.nextstrain.org

  Public
  Umbrella documentation project for Nextstrain

  Python

  •13•18•22•6•Updated Nov 26, 2024Nov 26, 2024

• mpox

  Public
  Nextstrain build for mpox virus

  metadatabioinformaticspipeline+ 10pathogenphylogeneticsgenbankaugurnextstrainauspicevirus-evolution+ 3

  Python

  •

  MIT License

  •19•45•26•8•Updated Nov 26, 2024Nov 26, 2024

• .github

  Public
  Shell

  •11•8•8•1•Updated Nov 26, 2024Nov 26, 2024

• zika

  Public
  Nextstrain build for Zika virus

  pathogennextstrain

  Python

  •11•8•3•0•Updated Nov 26, 2024Nov 26, 2024

• whitepaper

  Public
  White paper describing Nextstrain

  TeX

  •3•0•0•0•Updated Nov 26, 2024Nov 26, 2024

• infra

  Public
  Nextstrain shared infrastructure

  Makefile

  •0•0•2•0•Updated Nov 26, 2024Nov 26, 2024

• human-metapneumovirus

  Public
  Human metapneumovirus pathogen build

  Python

  •0•0•0•0•Updated Nov 26, 2024Nov 26, 2024

• pathogen-repo-guide

  Public template
  Python

  •1•4•18•0•Updated Nov 26, 2024Nov 26, 2024

• augur

  Public
  Pipeline components for real-time phylodynamic analysis

  Python

  •

  GNU Affero General Public License v3.0

  •128•268•244•55•Updated Nov 25, 2024Nov 25, 2024

• lassa

  Public
  Nextstrain build for Lassa virus

  pathogennextstrain

  Python

  •5•0•8•1•Updated Nov 25, 2024Nov 25, 2024

• avian-flu

  Public
  Nextstrain build for avian influenza viruses

  pathogennextstrain

  Python

  •8•21•11•5•Updated Nov 25, 2024Nov 25, 2024

• seasonal-flu

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

  pathogennextstrain

  Python

  •27•45•26•2•Updated Nov 23, 2024Nov 23, 2024

• nextstrain.org

  Public
  The Nextstrain website

  JavaScript

  •

  GNU Affero General Public License v3.0

  •48•89•82•12•Updated Nov 23, 2024Nov 23, 2024

• auspice

  Public
  Web app for visualizing pathogen evolution

  JavaScript

  •

  GNU Affero General Public License v3.0

  •162•292•240•54•Updated Nov 23, 2024Nov 23, 2024

• public

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

  0•0•9•1•Updated Nov 22, 2024Nov 22, 2024

• zika-tutorial

  Public
  Data and scripts for Zika virus tutorial

  Python

  •27•10•0•2•Updated Nov 22, 2024Nov 22, 2024

• conda-base

  Public
  Conda package build for nextstrain-base

  condamambanextstrain

  Shell

  •1•1•7•2•Updated Nov 22, 2024Nov 22, 2024

• WNV

  Public
  the repository used to build West Nile Virus for nextstrain

  pathogennextstrain

  Python

  •0•2•7•0•Updated Nov 22, 2024Nov 22, 2024

• ncov-clades-schema

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

  phylogeneticsnextstrainsars-cov-2+ 1clades

  JavaScript

  •8•10•4•4•Updated Nov 21, 2024Nov 21, 2024

• bioconda-recipes

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

  Shell

  •3.3k•0•3•0•Updated Nov 20, 2024Nov 20, 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•110•19•Updated Nov 20, 2024Nov 20, 2024

• ncov

  Public
  Nextstrain build for novel coronavirus SARS-CoV-2

  pathogennextstrainncov+ 1sars-cov-2

  Python

  •

  MIT License

  •403•1.4k•70•22•Updated Nov 19, 2024Nov 19, 2024

• fauna

  Public
  RethinkDB database to support real-time virus analysis

  Python

  •

  GNU Affero General Public License v3.0

  •13•33•19•10•Updated Nov 19, 2024Nov 19, 2024

• zika-tutorial-nextflow

  Public
  Nextflow based pipeline for Zika tutorial

  Nextflow

  •5•6•0•0•Updated Nov 19, 2024Nov 19, 2024

• auspice.us

  Public
  JavaScript

  •8•13•6•1•Updated Nov 19, 2024Nov 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•10•7•Updated Nov 19, 2024Nov 19, 2024

• status

  Public
  Nextstrain status pages

  JavaScript

  •0•1•6•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