Sep18 workshop day 1

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