Pekosz Lab Seasonal Influenza Nextstrain Builds 🦠

This repository turns influenza sequences from the Johns Hopkins Hospital (JHH) network into Nextstrain builds for JH-CEIRR: 24 segment builds (all 8 segments of H1N1, H3N2 and B/Victoria), 3 whole-genome builds, and a surveillance report. One Snakemake command runs everything, so the lab can track circulating clades season after season.

Live builds:

• nextstrain.org/groups/PekoszLab (lab members) ·
• nextstrain.org/groups/PekoszLab-Public (public)

Tip

📖 Full documentation lives on the Wiki: setup, step-by-step guides, tutorials, best practices and data rules.

flowchart LR
    A["Run FASTAs +<br/>GISAID vaccine strains"] --> B["source/<br/>3 input files"]
    B --> C["Config<br/>config/*.yaml"]
    C --> D["Snakemake:<br/>ingest + Nextclade"]
    D --> E["Augur:<br/>filter, align, tree, refine"]
    E --> F["Auspice JSONs<br/>auspice/"]
    E --> G["Reports<br/>reports/ + .run/"]
    F --> H["Review, then upload<br/>by hand"]

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Clone & get started

1. install conda

2. in your terminal execute:

git clone https://github.com/Pekosz-Lab/nextstrain.git && cd nextstrain
bash scripts/build_env.sh               # environment + checks + data-protection hooks
conda activate pekosz-nextstrain
snakemake --profile profiles/default --cores 8 --configfile config/tutorial.yaml

That runs the practice dataset. Details and real data: Getting Started → Tutorial 1.

Important

This repository is public and contains no data. It processes licensed GISAID sequences and unpublished JHH sequences, which must never be committed or shared. Read Data Protection before using real data. AI coding agents follow .agents/AGENTS.md.

Cite this software with CITATION.cff. Inspired by the Nextstrain team's seasonal-flu build.