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Pekosz Lab Seasonal Influenza Nextstrain Wiki 🦠

Welcome! This pipeline turns influenza sequences from the Johns Hopkins Hospital (JHH) network into Nextstrain builds: interactive family trees of the viruses circulating in Baltimore. It makes 24 segment builds (all 8 genome segments of H1N1, H3N2 and B/Victoria), 3 whole-genome builds, and a surveillance report for the lab, all with one command. You do not need any Nextstrain experience to start: follow the pages in order and you will have your first build running within the hour.

flowchart LR
    A["Raw run FASTAs<br/>+ GISAID vaccine strains"] --> B["source/<br/>3 input files"]
    B --> C["Config<br/>config/*.yaml"]
    C --> D["Snakemake run<br/>ingest + Nextclade"]
    D --> E["Augur steps<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 to Nextstrain"]

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The whole pipeline at a glance: data is prepared into source/, Snakemake runs every step, and a person reviews the trees before anything is published.

Start here

If you want to...	Go to
Install everything	Getting Started
Run the pipeline once on practice data	Tutorial 1: Your First Build
Understand what each stage does	Pipeline Overview

The pipeline, in order

1. Step 1: Source Data Preparation: build the source/ folder
2. Step 2: Running the Pipeline: commands, options, runtime
3. Step 3: Filtering & Quality Control: what removes a sequence, and where
4. Step 4: Reports & Outputs: what you get and how to read it
5. Step 5: Reviewing & Publishing Builds: check, then upload by hand

Tutorials (hands-on)

• Tutorial 1: Your First Build
• Tutorial 2: Adding a New Sequencing Run
• Tutorial 3: Updating Vaccine Strains from GISAID

Reference

• Best Practices: checklists for changes, code, git and sharing
• Data Protection: GISAID & JHH: read before you touch real data
• Snakemake & Scripts Reference
• How are clade and subclade colors handled: from Nextclade call to legend color
• Coding with Agents: policy for AI-assisted development
• Glossary
• Roadmap & Known Issues

Important

For lab leadership (no technical background needed). Two kinds of data go in, and both are restricted: GISAID vaccine-strain sequences (licensed; never published or passed to anyone without their own GISAID access) and JHH sequences (private until the Mostafa Lab releases them). The code is public on GitHub; the data never is. Automatic checks stop anyone from uploading that data to GitHub by mistake, and nothing is published to Nextstrain without a trained person inspecting it first. Dr. Pekosz decides who may change the filters or the pipeline, what goes to the public Nextstrain page, and who receives the confidential surveillance report.

Live builds

• Private (lab members): https://nextstrain.org/groups/PekoszLab
• Public: https://nextstrain.org/groups/PekoszLab-Public

Where to get help

For	Who
Sequencing files, run dates, which FASTA to use	Dr. Heba Mostafa (Mostafa Lab)
Access to data, contamination warnings, scientific questions, public uploads	Dr. Andy Pekosz (apekosz1@jh.edu); lab data: Step 1
Pipeline errors, code changes, this wiki	Pipeline maintainer: Elgin Akin ([ADD JHU EMAIL]; GitHub @elginakin) until handover; update at handover

Acknowledgements

Automation with Snakemake has increased the efficiency of these builds. The structure, scripts and configuration files are strongly inspired by the seasonal-flu build maintained by the Nextstrain team. Cite this software with CITATION.cff.

Troubleshooting / FAQ

• A page here disagrees with the code. The code wins. Tell the maintainer, or fix the page in the same pull request as your code change (Coding with Agents).
• I can't see the private builds. Ask the maintainer to add you to the PekoszLab Nextstrain group.
• Diagrams don't render. Mermaid diagrams render on github.com; in a local editor, install a Mermaid preview extension.

Next step → Getting Started