Reconstructing transmission with genomic data

Module 7 SISMID 2023, July 17-19, Caroline Colijn and Jessica Stockdale

Project maintained by jessicastockdale Hosted on GitHub Pages — Theme by mattgraham

Welcome to ‘Reconstructing Transmission with Genomic Data’ at SISMID 2023

This site hosts all of the online materials for the course.

For more details see our module page on the SISMID website.


The schedule is available here.

Things to know

Module Preparation

All computational exercises in this module will use R and Rstudio.

If you’ve never used R before, we have created a tutorial for you to work through in advance of the course. If you’ve already done a tutorial for one of the other SISMID modules or otherwise, that will be fine too. You can access the tutorial here: An Introduction to R and RStudio.

We have also created a short second R tutorial which walks you through installing all of the packages we’ll be using during the module. Please work through this in advance of the course. If you have any problems, feel free to drop us a message on Slack. The second tutorial can be accessed here: Installation and preparation instructions. Note: everyone should do this one!

In addition, for participants new to genomic sequencing and genomic data, we ask you to watch the following Youtube lecture in advance of the course, which provides a short primer on relevant aspects of the field to our course

Exercise materials

Here you will be able to download the course exercise materials. Click each link to download data files and access exercise instructions. Links to solutions will be added once the exercises are complete.

Exercise 1: Data, Instructions, Tips, and Solutions.

Exercise 2: Instructions, Extra Helper Code and Solutions: COVID-19, TB.

Exercise 3: Data, Instructions, Extension exercise and Solutions: COVID-19, TB.

Exercise 4: Instructions, TransPhylo Extra Code and Solutions: COVID-19, TB.

Data for exercises 2, 3, 4: TB data. COVID-19 data will be provided on Slack.

Lecture slides

Here you will be able to download the lecture slides.

Lecture 1

Lecture 2

Lecture 3

Lecture 4

Lecture 5

Resources/reading list

For a list of papers/websites/books we either mentioned during the course or just think you might find interesting, check out the resources list


You can contact us at:

Caroline Colijn:
Jessica Stockdale: