Simulation Exercises

The SeqAfrica project invites current and past consortium members, members of the Africa CDC's Pathogen Genomics Initiative network, members of the SARA network, Fleming Fund Country Grant participants and Fleming Fund Fellows to join a training workshop on an AMR outbreak detection using simulation exercises and genomic tools. A simulation exercise can help develop, assess, and test functional capabilities of emergency systems, procedures, and mechanisms to be able to respond to outbreaks or public health emergencies.

​The simulation exercises provide a supporting background for performing various steps of outbreak investigations with a special focus on the use of whole genome sequencing (WGS) based methods  for bacterial typing and outbreak detection. The training workshop will be held as an exercise concerning a fictitious outbreak, with data released over time in the form of data injects form different departments at a hospital, to simulate a possible outbreak situation.


The objective of this exercise is to provide the supporting background for performing various steps of an outbreak investigation with a focus on the use of WGS-based methods for bacterial typing and outbreak detection. Participants will learn about principles and methodologies for sub-typing and cluster analysis to be able to detect outbreaks and will be equipped to investigate outbreaks by leveraging on multidisciplinary collaboration.

Who should participate?

Team of microbiology, healthcare epidemiology, and bioinformatics experts are encouraged to participate. Management level representatives from laboratories that do not use WGS are also encouraged to participate so that they can learn about the utility and added value of WGS-based methods for outbreak detection. Ideally, a group of colleagues from one laboratory will participate in the exercise. The exercise is focused on the participants with limited knowledge in bioinformatics and bacterial genomics.

Outline of the training workshop:

This workshop is divided into two online sessions of a maximum of two hours. The injects will be released four times (four data injects) with two question surveys in between the sessions.

A link for downloading sequence data will be distributed. The accessible sequence data will cover both Illumina (MiSeq/NextSeq) fast and fast files, as well as Oxford Nanopore (MinION) fast and fast files. The tools presented for the exercise will mainly be web-based tools and it should be possible to work with the exercise even with low computing capacity and with only basic knowledge about genome analysis. It will not be a requirement to work with MinION sequenced to complete the exercise.


​Dates to be determined for 2024 and 2025 and will be announced on this page once settled.

To join:

If your team is interested in joining a simulation exercise, please complete this survey.

If you/your team are not sure you are eligible to join, please reach out to us at



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