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This training is provided by ECDC as part of the GenEpi-BioTrain programme and is delivered by Technical University of Denmark. It is open for enrolment for anyone interested in learning more about genomic tools for outbreak investigations.

Why attend this training?

Participants will develop skills in interpreting genomic data for outbreak investigations, including phylogenetic tree construction, AMR profiling, and critical analysis of WGS results. The training provides hands-on experience with real-world data and a simulation exercise to deepen understanding.

Who is the training for?

Bioinformaticians, microbiologists, epidemiologists, and clinicians with basic bioinformatics skills.

How long is the training?

This virtual training consists of two sessions held on Wednesday 27 August, and Wednesday 3 September, from 9:00 to 12:30 (CEST).

• Session 1: Introduction to Molecular Epidemiology and WGS in Outbreak Investigation 
• Session 2: Interpretation of Results and Discussion on the Application of WGS in Outbreak Scenarios

Practical exercises will be assigned during Session 1 and should be completed before Session 2, where the results will be discussed.

Will the training be recorded?

Yes, when you enrol in the training, you will also get access to the recordings after the live sessions.

Can I get a certificate?

To get a certificate of completion, you need to attend at least one live session and to watch the recording of the other session you were not able to attend.

What are the requirements for the practical exercises?

Participants should read the 'Software requirements' carefully and prepare the necessary tools before the first session. 

For the practical exercises, participants need to use the following software: Snippy, CSI Phylogeny, MINTyper, IQ-TREE, iTOL, AMRFinderPlus, ResFinder, CholeraFinder, IslandViewer, VCGIDB. More information on how to install them is available on the course page after you’ve enrolled.

Participants who do not meet the requirements may join as observers. 

How can I enrol?

You can access the training for free, thanks to EU funding.

Log in to the Learning Portal and enrol in the course.