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Nextstrain

Real-time tracking of pathogen evolution

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

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ncov ncov Public

Nextstrain build for SARS-CoV-2

Python 1.4k 409
augur augur Public

Pipeline components for real-time phylodynamic analysis

Python 275 136
auspice auspice Public

Web app for visualizing pathogen evolution

JavaScript 305 168

Repositories

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

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Showing 10 of 100 repositories

nextstrain.org Public
The Nextstrain website

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

JavaScript 95 AGPL-3.0 53 74 12 Updated Jan 27, 2026
chikv Public
Chikungunya virus workflows

nextstrain/chikv’s past year of commit activity

Python 1 0 0 0 Updated Jan 27, 2026
docs.nextstrain.org Public
Umbrella documentation project for Nextstrain

nextstrain/docs.nextstrain.org’s past year of commit activity

Python 18 13 25 3 Updated Jan 27, 2026
augur Public
Pipeline components for real-time phylodynamic analysis

nextstrain/augur’s past year of commit activity

Python 275 AGPL-3.0 136 233 (1 issue needs help) 39 Updated Jan 27, 2026
bioconda-recipes Public Forked from bioconda/bioconda-recipes
Fork for maintaining Nextstrain-related recipes and submitting PRs upstream.

nextstrain/bioconda-recipes’s past year of commit activity

Shell 0 3,745 3 0 Updated Jan 26, 2026
nextclade_data Public
Datasets for https://github.com/nextstrain/nextclade

nextstrain/nextclade_data’s past year of commit activity

Python 43 41 9 17 Updated Jan 26, 2026
mpox Public
Nextstrain build for mpox virus

nextstrain/mpox’s past year of commit activity

Python 50 MIT 23 17 8 Updated Jan 26, 2026
nextclade Public
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement

nextstrain/nextclade’s past year of commit activity

TypeScript 250 MIT 66 120 (34 issues need help) 30 Updated Jan 26, 2026
seasonal-flu Public
Scripts. config, and snakefiles for seasonal-flu nextstrain builds

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

Python 57 29 31 10 Updated Jan 26, 2026
measles Public
Nextstrain build for measles virus

nextstrain/measles’s past year of commit activity

Python 3 8 7 9 Updated Jan 23, 2026

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nextstrain pathogen sars-cov-2 clades ncov

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