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Nextstrain

Real-time tracking of pathogen evolution

219 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 305 170

Repositories

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Showing 10 of 100 repositories

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

nextstrain/nextclade_data’s past year of commit activity

Python 44 42 9 17 Updated Mar 6, 2026
seasonal-flu Public
Scripts. config, and snakefiles for seasonal-flu nextstrain builds

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

Python 58 29 31 9 Updated Mar 6, 2026
rsv Public
Workflow for RSV analyses on Nextstrain.org

nextstrain/rsv’s past year of commit activity

Python 11 8 9 5 Updated Mar 6, 2026
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.

nextstrain/ncov-ingest’s past year of commit activity

Python 37 MIT 20 33 9 Updated Mar 5, 2026
nextclade Public
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement

nextstrain/nextclade’s past year of commit activity

TypeScript 252 MIT 66 123 (34 issues need help) 30 Updated Mar 5, 2026
mumps Public
Nextstrain build for mumps virus

nextstrain/mumps’s past year of commit activity

Python 2 7 5 3 Updated Mar 5, 2026
rubella Public
Nextstrain build for rubella virus

nextstrain/rubella’s past year of commit activity

Python 2 2 3 2 Updated Mar 5, 2026
hmpv Public
Human metapneumovirus pathogen build

nextstrain/hmpv’s past year of commit activity

Python 0 0 5 0 Updated Mar 5, 2026
nextstrain.org Public
The Nextstrain website

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

JavaScript 96 AGPL-3.0 54 71 12 Updated Mar 5, 2026
augur Public
Pipeline components for real-time phylodynamic analysis

nextstrain/augur’s past year of commit activity

Python 275 AGPL-3.0 136 234 (1 issue needs help) 39 Updated Mar 5, 2026

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