Lectures and materials for GS541 Introduction to Computational Molecular Biology

GENOME 541 Introduction to Computational Molecular Biology

Day 1

Motivation: we can learn about outbreaks by sequencing infecting pathogens.

Introduction: Phylodynamics and application to SARS-CoV-2

Lecture 1: Molecular clocks and the coalescent

Day 2

Lecture 2: Discrete traits and phylogeography

Homework

This homework will focus on using Nextstrain to infer global phylogeography of SARS-CoV-2.

Start by installing Nextstrain by following these instructions: https://nextstrain.org/docs/getting-started/quickstart. Slightly confusingly, we have two ways to get software installed. If you can run Docker on your computer, the "container-based" installation should be easier and is what's recommended by the quickstart. If Docker is giving you problems, you should try the "local" installation that relies on Conda.

You should check that the installation is working by running the "Zika tutorial" described here with:

Once things are correctly installed, download the "ncov" repository here: github.com/nextstrain/ncov. There is an example dataset in example_data. To get this in place run:

  • mkdir data
  • cp example_data/* data/

To make things run faster, open the file config/config.yml and change sequences_per_group under filter from 2000 to 10. Then, run the build with:

  • nextstrain build . (container-based installation) or snakemake -p (local installation)

This will complete in ~10 minutes. You can then view results with:

  • nextstrain view auspice/ (container-based installation) or auspice view --datasetDir auspice (local installation)

Open a browser to http://127.0.0.1:4000 (container-based installation) or http://localhost:4000 (local installation) to view the results.

Next:

  • Create a new GitHub public repository on your personal account titled gs541-phylogeography.
  • Rename the file auspice/ncov_global.json generated above to auspice/gs541-phylogeography.json and commit to this repository.
  • Doing so will make the link nextstrain.org/community/{your-github-username}/gs541-phylogeography display this Auspice file.

For the assignment, please upload:

  1. A link to your GitHub repository for gs541-phylogeography and a link to your community Nextstrain page. 30 points
  2. A paragraph write-up that describes your interpretation of the transmission history from an individual country or state from nextstrain.org/ncov (your choice). You can filter to a specific state by clicking under "Filter by Admin Division" here: nextstrain.org/ncov/north-america?c=division&r=division. For countries outside North America, I'd recommend using a region specific build: Africa, Asia, Europe, Oceania, South America. You can filter to a specific country by clicking under "Filter by County". 30 points