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: Kwong et al 2016 (WGS for national surveillance of Listeria) 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: The raw data, assembly, and quality measures

Readings: Jünemann et al 2014 (Comparing assemblers) PDF

Slides: PDF

Instructions: Read trimming using PRINSEQ 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: Zankari et al 2017 (PointFinder/ResFinder-3.0) PDF

Readings: Hasman et al 2015 (Colistin in Denmark 2015) PDF

Readings: Carattoli et al 2014 (PlasmidFinder and pMLST paper) PDF

Slides: PDF

14:15-14:30: Introduction to Exercise 1

Readings: Grad et al 2012 (German E. coli outbreak) PDF

Slides: PDF

13:45-15:00: Computer work w. single isolates and single services

Exercise1

15:45-16:00: Coffee break

16:00-16:30: Exercise 1 continued

16:30-17:00: Wrap-up of computerwork

Slides: PDF