Skip to content

Navigation Menu

Appearance settings

View all features
- BY COMPANY SIZE
  Enterprises
  Small and medium teams
  Startups
  Nonprofits
- BY USE CASE
  App Modernization
  DevSecOps
  DevOps
  CI/CD
  View all use cases
- BY INDUSTRY
  Healthcare
  Financial services
  Manufacturing
  Government
  View all industries
View all solutions
- EXPLORE BY TOPIC
  AI
  Software Development
  DevOps
  Security
  View all topics
- EXPLORE BY TYPE
  Customer stories
  Events & webinars
  Ebooks & reports
  Business insights
  GitHub Skills
- SUPPORT & SERVICES
  Documentation
  Customer support
  Community forum
  Trust center
  Partners
View all resources
- COMMUNITY
  GitHub SponsorsFund open source developers
- PROGRAMS
  Security Lab
  Maintainer Community
  GitHub Stars
  Archive Program
- REPOSITORIES
  Topics
  Trending
  Collections
- ENTERPRISE SOLUTIONS
  Enterprise platformAI-powered developer platform
- AVAILABLE ADD-ONS
  GitHub Advanced SecurityEnterprise-grade security features
  Copilot for BusinessEnterprise-grade AI features
  Premium SupportEnterprise-grade 24/7 support
Pricing

Appearance settings

You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session.

Dismiss alert

Nextstrain

Real-time tracking of pathogen evolution

237 followers
https://nextstrain.org
@nextstrain
@nextstrain@mstdn.science

Overview
Repositories
Projects
Packages
People

More

Overview
Repositories
Projects
Packages
People

Pinned Loading

ncov ncov Public

Nextstrain build for SARS-CoV-2

Python 1.4k 408
augur augur Public

Pipeline components for real-time phylodynamic analysis

Python 279 137
auspice auspice Public

Web app for visualizing pathogen evolution

JavaScript 312 172

Repositories

Loading

Type

Select type

All Public Sources Forks Archived Mirrors Templates

Language

Select language

All C Dockerfile Go HTML JavaScript Jupyter Notebook Makefile Nextflow Perl Python R Rust Shell TeX TypeScript WDL

Sort

Select order

Last updated Name Stars

Showing 10 of 105 repositories

augur Public
Pipeline components for real-time phylodynamic analysis

nextstrain/augur's past year of commit activity

Python 279 AGPL-3.0 137 231 (1 issue needs help) 43 Updated Oct 2, 2026
ncov Public
Nextstrain build for SARS-CoV-2

nextstrain/ncov's past year of commit activity

Python 1,362 MIT 408 69 19 Updated Oct 2, 2026
nextclade Public
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement

nextstrain/nextclade's past year of commit activity

Rust 263 MIT 68 119 39 Updated Oct 2, 2026
shared Public
Shared internal tooling for pathogen workflows. Used by our individual pathogen repos which produce Nextstrain builds.

nextstrain/shared's past year of commit activity

Python 1 1 4 4 Updated Oct 1, 2026
infra Public
Nextstrain shared infrastructure

nextstrain/infra's past year of commit activity

Makefile 0 0 2 0 Updated Oct 1, 2026
seasonal-flu Public
Scripts. config, and snakefiles for seasonal-flu nextstrain builds

nextstrain/seasonal-flu's past year of commit activity

Python 65 34 28 8 Updated Oct 1, 2026
forecasts-flu Public
Seasonal influenza variant growth rates and frequency forecasts

nextstrain/forecasts-flu's past year of commit activity

Python 2 MIT 0 11 2 Updated Oct 1, 2026
nextstrain.org Public
The Nextstrain website

nextstrain/nextstrain.org's past year of commit activity

JavaScript 96 AGPL-3.0 56 72 14 Updated Oct 1, 2026
nextclade_data Public
Datasets for https://github.com/nextstrain/nextclade

nextstrain/nextclade_data's past year of commit activity

Python 47 44 11 19 Updated Oct 1, 2026
ebola Public
Nextstrain build for Ebola virus

nextstrain/ebola's past year of commit activity

Python 6 10 9 1 Updated Oct 1, 2026

View all repositories

People

Top languages

Loading…

Uh oh!

There was an error while loading. Please reload this page.

Most used topics

nextstrain pathogen sars-cov-2 clades ncov

Footer

© 2026 GitHub, Inc.

Footer navigation

Terms
Privacy
Security
Status
Community
Docs
Contact

You can’t perform that action at this time.