- augur Public
Pipeline components for real-time phylodynamic analysis
nextstrain/augur’s past year of commit activity
- infra Public
Nextstrain shared infrastructure
nextstrain/infra’s past year of commit activity
Makefile 0 0
2 2
Updated Jun 12, 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 32 10
Updated Jun 12, 2026
- seasonal-flu Public
Scripts. config, and snakefiles for seasonal-flu nextstrain builds
nextstrain/seasonal-flu’s past year of commit activity
Python
62 31 26 7
Updated Jun 12, 2026
- avian-flu Public
Nextstrain build for avian influenza viruses
nextstrain/avian-flu’s past year of commit activity
Python
28 10 18 6
Updated Jun 12, 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 Nextstrain components like Augur and Auspice across computing environments such as Docker, Conda, and AWS Batch.
nextstrain/cli’s past year of commit activity
Python
28
MIT
20 69 3
Updated Jun 12, 2026
- measles Public
Nextstrain build for measles virus
nextstrain/measles’s past year of commit activity
Python
4 9 7 6
Updated Jun 12, 2026
- nextstrain/bioconda-recipes’s past year of commit activity
Shell 0
3,990 3 0
Updated Jun 12, 2026
- mpox Public
Nextstrain build for mpox virus
nextstrain/mpox’s past year of commit activity
Python
50
MIT
22 17 8
Updated Jun 12, 2026
- nextstrain/auspice.us’s past year of commit activity
JavaScript
13 8 7 3
Updated Jun 11, 2026