SISMID 2026 · Lab Sessions
Reconstructing Transmission with Genomic Data
Synchronous lab sessions — June 25–26, 2026
Below you will find materials and recordings for each of your four lab sessions. Materials may be added before or after each session by your instructors.
About the lab sessions
1
Transmission Reconstruction with Outbreaker
Get hands-on experience using Outbreaker. After a guided tutorial, you will have the opportunity to apply Outbreaker to one of two real-world datasets, to infer who-infected-whom.
2
Transmission Reconstruction with TransPhylo
In this lab, we will work together on the TransPhylo model. You’ll be able to compare your findings against those from Lab 1.
3
Transmission Reconstruction with BREATH
Lastly, we’ll work with BREATH. A similar process will guide you through a tutorial, before challenging you to infer who infected whom from real-world data.
4
Transmission Reconstruction – Pulling it all Together
Our final lab will provide extra time for finishing previous work, and the opportunity to compare and contrast your findings. We will think about how the results of transmission reconstruction are presented, e.g. options for graphing, and how to extract answers to common public health questions. Dedicated Q&A time will allow you to ask questions from the module or from your own research projects.
Lab sessions