A two-part tutorial for the Pekosz Lab Nextstrain Influenza Builds

This tutorial runs the Pekosz Lab influenza workflow with a small teaching dataset containing 20 H1N1, 20 H3N2, and 20 B/Victoria strains generated by Dr. Heba Mostafa’s Lab at the Johns Hopkins Hospital.

Author

Affiliation

Elgin Akin

Johns Hopkins University

What is Nextstrain and how do we use it?

Nextstrain is a powerful open-source platform for building, hosting, and interacting with phylogenies. The Pekosz Lab leverages this platform to facilitate discussions sorrounding emerging Influenza A and B variants during genomic surveillance each influenza season. Please refer to the extensive Nextstrain Documentation for a more comprehensive overview.

Pekosz lab Nextstrain Builds are hosted by the Nextstrain team at the following locations:

• A private site for internal surveillance meetings:
  • https://nextstrain.org/groups/PekoszLab (contact apekosz1@jh.edu for access)
• A publically hosted website for publications:
  • https://nextstrain.org/groups/PekoszLab-Public
• All code necessary to run both this tutorial and the pipline with “real world” data from the Mostafa lab can be found here:
  • https://github.com/Pekosz-Lab/nextstrain/tree/main

Tutorial Resources

Note

This tutorial is optimized to run on machines running MacOS. Users who desire to run this pipeline on Windows must refer to the WSL installation documentation provided by Nextstrain.

The Pekosz Lab incorperates Influenza sequences generated by the Mostafa Lab using a semi-automated preparation pipeline, outlined in Part 2, and a fully automated pipeline outline in Part 1.

Tutorial Part 1 - Downloading dependencies, building your environment, and running the tutorial dataset

Part 1 includes a small example dataset of influenza sequences and associated metadata for both training and testing of the fully automated pipeline.

• Part 1 Tutorial Slides

• Part 1 Written Tutorial

Tutorial Part 2 - Preparing and incorporating data generated by the Mostafa Lab

Part 2 provides instructions on how to curate the sequences.fasta and metadata.txt files and how to incorperate new runs into these builds.

• Part 2 Tutorial Slides