9:30-10:00: Registration and breakfast
10:00-10:15: Welcome and presentation round
Readings: Quainoo et al 2017 (WGS is the future of nosocomial outbreak analysis) PDF
Slides: PDF
10:15-11:15: Sequencing techniques
Slides (1st half): PDF
Slides (2nd half): PDF
Multiple choice questions (for self-evaluation) PDF
11:15-11:30: Coffee
11:30-12:30: Assembly and quality measures
Readings: Jünemann et al 2014 (Comparing assemblers) PDF
Slides: PDF
12:30-13:30: Lunch
13:30-14:15: Intro to single-isolates, single CGE services
Readings: The CGE tool box (chapter 5 from Applied Genomics of Foodborn Pathogens describing tools in the CGE tool box) PDF
Readings: Larsen et al 2014 (paper on benchmarking of methods for genomic taxonomy) PDF
Readings: Larsen et al 2012 (MLST paper) PDF
Readings: Zankari et al 2012 (ResFinder-1.0) PDF
Readings: Carattoli et al 2014 (PlasmidFinder and pMLST paper) PDF
Slides: PDF
14:15-15:00: Computer work w. single isolates and single services
15:00-15:15: Coffee break
15:15-16:30: Exercise 1 continued
16:30-17:00: Wrap-up of computerwork
Slides: PDF