Nextstrain (original) (raw)

• 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