Mar18 workshop day 1

9:30-10:00: Registration and breakfast

10:00-10:30: Welcome and presentation round

Slides: PDF

10:30-10:45: Introduction to Whole Genome Sequencing and its applications in microbial diagnostics

Readings: Quainoo et al 2017 (WGS is the future of nosocomial outbreak analysis) PDF

Readings: Votintseva et al 2017 (Same day TB diagnostics) PDF

Readings: Mellmann et al 2016 (WGS in hospital setting) PDF

Slides: PDF

10:45-11:30: Sequencing techniques

Slides: PDF

Multiple choice questions (for self-evaluation) PDF

11:30-11:45: Coffee

11:45-12:30: 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

15:15-16:45: Exercise 1 continued

16:45-17:00: Wrap-up of computerwork

Slides: PDF