Repositories list

• docs.nextstrain.org

  Public
  Umbrella documentation project for Nextstrain

  Python

  •1313 forks in nextstrain/docs.nextstrain.org•1818 stars in nextstrain/docs.nextstrain.org•2626 issues in nextstrain/docs.nextstrain.org•44 pull requests in nextstrain/docs.nextstrain.org•Updated Nov 7, 2026Nov 7, 2026

• nextstrain.org

  Public

  nextstrain/nextstrain.org’s past year of commit activity
  The Nextstrain website

  JavaScript

  •

  GNU Affero General Public License v3.0

  •5858 forks in nextstrain/nextstrain.org•9696 stars in nextstrain/nextstrain.org•7171 issues in nextstrain/nextstrain.org•1414 pull requests in nextstrain/nextstrain.org•Updated Nov 6, 2026Nov 6, 2026

• ebola

  Public

  nextstrain/ebola’s past year of commit activity
  Nextstrain build for Ebola virus

  pathogennextstrain

  pathogennextstrain

  Python

  •1111 forks in nextstrain/ebola•77 stars in nextstrain/ebola•1212 issues in nextstrain/ebola•33 pull requests in nextstrain/ebola•Updated Nov 6, 2026Nov 6, 2026

• auspice

  Public

  nextstrain/auspice’s past year of commit activity
  Web app for visualizing pathogen evolution

  JavaScript

  •

  GNU Affero General Public License v3.0

  •172172 forks in nextstrain/auspice•312312 stars in nextstrain/auspice•246246 issues in nextstrain/auspice•4343 pull requests in nextstrain/auspice•Updated Nov 5, 2026Nov 5, 2026

• seasonal-flu

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

  pathogennextstrain

  pathogennextstrain

  Python

  •3434 forks in nextstrain/seasonal-flu•6565 stars in nextstrain/seasonal-flu•2727 issues in nextstrain/seasonal-flu•99 pull requests in nextstrain/seasonal-flu•Updated Nov 5, 2026Nov 5, 2026

• 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 N…

  Python

  •

  MIT License

  •2020 forks in nextstrain/cli•2828 stars in nextstrain/cli•7171 issues in nextstrain/cli•66 pull requests in nextstrain/cli•Updated Nov 5, 2026Nov 5, 2026

• .github

  Public

  nextstrain/.github’s past year of commit activity
  Shell

  •1212 forks in nextstrain/.github•99 stars in nextstrain/.github•1212 issues in nextstrain/.github•00 pull requests in nextstrain/.github•Updated Nov 5, 2026Nov 5, 2026

• docker-base

  Public
  Docker image build for nextstrain/base

  Shell

  •88 forks in nextstrain/docker-base•1212 stars in nextstrain/docker-base•77 issues in nextstrain/docker-base•11 pull request in nextstrain/docker-base•Updated Nov 5, 2026Nov 5, 2026

• nextclade

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

  scienceresearchvirus+ 17

  scienceresearchvirussequencingnext-generation-sequencingdnarnainfluenzasequencesstrain+ 10

  Rust

  •

  MIT License

  •6969 forks in nextstrain/nextclade•265265 stars in nextstrain/nextclade•123123 issues in nextstrain/nextclade•3232 pull requests in nextstrain/nextclade•Updated Nov 5, 2026Nov 5, 2026

• augur

  Public

  nextstrain/augur’s past year of commit activity
  Pipeline components for real-time phylodynamic analysis

  Python

  •

  GNU Affero General Public License v3.0

  •139139 forks in nextstrain/augur•280280 stars in nextstrain/augur•229229 issues in nextstrain/augur•4242 pull requests in nextstrain/augur•Updated Nov 5, 2026Nov 5, 2026

• zika-tutorial

  Public
  Data and scripts for Zika virus tutorial

  Python

  •3030 forks in nextstrain/zika-tutorial•1010 stars in nextstrain/zika-tutorial•00 issues in nextstrain/zika-tutorial•11 pull request in nextstrain/zika-tutorial•Updated Nov 4, 2026Nov 4, 2026

• forecasts-flu

  Public
  Seasonal influenza variant growth rates and frequency forecasts

  pathogennextstrain

  pathogennextstrain

  Python

  •

  MIT License

  •00 forks in nextstrain/forecasts-flu•22 stars in nextstrain/forecasts-flu•1212 issues in nextstrain/forecasts-flu•22 pull requests in nextstrain/forecasts-flu•Updated Nov 4, 2026Nov 4, 2026

• variant-nowcast-hub

  Public
  A repository to store COVID-19 variant nowcasts collected as a modeling hub.

  R

  •

  MIT License

  •1717 forks in nextstrain/variant-nowcast-hub•00 stars in nextstrain/variant-nowcast-hub•00 issues in nextstrain/variant-nowcast-hub•00 pull requests in nextstrain/variant-nowcast-hub•Updated Nov 4, 2026Nov 4, 2026

• nextclade_data

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

  Python

  •4444 forks in nextstrain/nextclade_data•4747 stars in nextstrain/nextclade_data•1111 issues in nextstrain/nextclade_data•2020 pull requests in nextstrain/nextclade_data•Updated Nov 4, 2026Nov 4, 2026

• bioconda-recipes

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

  Shell

  •4.2k4.2k forks in nextstrain/bioconda-recipes•00 stars in nextstrain/bioconda-recipes•33 issues in nextstrain/bioconda-recipes•00 pull requests in nextstrain/bioconda-recipes•Updated Nov 4, 2026Nov 4, 2026

• rsv

  Public
  Workflow for RSV analyses on Nextstrain.org

  pathogennextstrain

  pathogennextstrain

  Python

  •99 forks in nextstrain/rsv•1111 stars in nextstrain/rsv•99 issues in nextstrain/rsv•44 pull requests in nextstrain/rsv•Updated Nov 2, 2026Nov 2, 2026

• avian-flu

  Public
  Nextstrain build for avian influenza viruses

  pathogennextstrain

  pathogennextstrain

  Python

  •1111 forks in nextstrain/avian-flu•2929 stars in nextstrain/avian-flu•1818 issues in nextstrain/avian-flu•55 pull requests in nextstrain/avian-flu•Updated Nov 2, 2026Nov 2, 2026

• rubella

  Public
  Nextstrain build for rubella virus

  pathogennextstrain

  pathogennextstrain

  Python

  •22 forks in nextstrain/rubella•22 stars in nextstrain/rubella•77 issues in nextstrain/rubella•44 pull requests in nextstrain/rubella•Updated Nov 2, 2026Nov 2, 2026

• WNV

  Public
  the repository used to build West Nile Virus for nextstrain

  pathogennextstrain

  pathogennextstrain

  Python

  •33 forks in nextstrain/WNV•55 stars in nextstrain/WNV•77 issues in nextstrain/WNV•11 pull request in nextstrain/WNV•Updated Oct 30, 2026Oct 30, 2026

• auspice.us

  Public
  JavaScript

  •88 forks in nextstrain/auspice.us•1313 stars in nextstrain/auspice.us•44 issues in nextstrain/auspice.us•00 pull requests in nextstrain/auspice.us•Updated Oct 29, 2026Oct 29, 2026

• ncov

  Public
  Nextstrain build for SARS-CoV-2

  pathogennextstrainncov+ 1

  pathogennextstrainncovsars-cov-2

  Python

  •

  MIT License

  •408408 forks in nextstrain/ncov•1.4k1.4k stars in nextstrain/ncov•7171 issues in nextstrain/ncov•1919 pull requests in nextstrain/ncov•Updated Oct 27, 2026Oct 27, 2026

• conda-base

  Public
  Conda package build for nextstrain-base

  condamambanextstrain

  condamambanextstrain

  Shell

  •11 fork in nextstrain/conda-base•11 star in nextstrain/conda-base•44 issues in nextstrain/conda-base•11 pull request in nextstrain/conda-base•Updated Oct 26, 2026Oct 26, 2026

• mpox

  Public
  Nextstrain build for mpox virus

  metadatabioinformaticspipeline+ 10

  metadatabioinformaticspipelinepathogenphylogeneticsgenbankaugurnextstrainauspicevirus-evolution+ 3

  Python

  •

  MIT License

  •2323 forks in nextstrain/mpox•5050 stars in nextstrain/mpox•1919 issues in nextstrain/mpox•99 pull requests in nextstrain/mpox•Updated Oct 26, 2026Oct 26, 2026

• enterovirus_d68

  Public
  Enterovirus-D68 phylogenetic analyses code - actively maintained

  Python

  •66 forks in nextstrain/enterovirus_d68•11 star in nextstrain/enterovirus_d68•11 issue in nextstrain/enterovirus_d68•00 pull requests in nextstrain/enterovirus_d68•Updated Oct 22, 2026Oct 22, 2026

• fauna

  Public
  RethinkDB database to support real-time virus analysis

  Python

  •

  GNU Affero General Public License v3.0

  •1212 forks in nextstrain/fauna•3636 stars in nextstrain/fauna•1919 issues in nextstrain/fauna•1010 pull requests in nextstrain/fauna•Updated Oct 21, 2026Oct 21, 2026

• narratives

  Public
  Narrative markdown files accessed via nextstrain.org/narratives/x

  Shell

  •1010 forks in nextstrain/narratives•33 stars in nextstrain/narratives•22 issues in nextstrain/narratives•11 pull request in nextstrain/narratives•Updated Oct 21, 2026Oct 21, 2026

• lassa

  Public
  Nextstrain build for Lassa virus

  pathogennextstrain

  pathogennextstrain

  Python

  •55 forks in nextstrain/lassa•44 stars in nextstrain/lassa•99 issues in nextstrain/lassa•22 pull requests in nextstrain/lassa•Updated Oct 19, 2026Oct 19, 2026

• infra

  Public
  Nextstrain shared infrastructure

  Makefile

  •00 forks in nextstrain/infra•00 stars in nextstrain/infra•22 issues in nextstrain/infra•11 pull request in nextstrain/infra•Updated Oct 15, 2026Oct 15, 2026

• pathogen-repo-guide

  Public template
  Python

  •11 fork in nextstrain/pathogen-repo-guide•55 stars in nextstrain/pathogen-repo-guide•2121 issues in nextstrain/pathogen-repo-guide•00 pull requests in nextstrain/pathogen-repo-guide•Updated Oct 15, 2026Oct 15, 2026

• zika

  Public
  Nextstrain build for Zika virus

  pathogennextstrain

  pathogennextstrain

  Python

  •1111 forks in nextstrain/zika•1212 stars in nextstrain/zika•55 issues in nextstrain/zika•22 pull requests in nextstrain/zika•Updated Oct 15, 2026Oct 15, 2026