Workshop day 1

9:00-9:30: Registration and breakfast

9:30-10:00: Welcome and presentation round

Slides: PDF

10:00-10:15: Short introduction to Whole Genome Sequencing and its applications in microbial diagnostics

Readings: Didelot et al 2012 (How whole genome sequencing will transform clinical microbiology) PDF

Readings: Inns et al 2015 (Salmonella outbreak in UK) PDF

Supplementary reading: Pathogen Genomics Into Practice (Book of general concepts) PDF

Slides: PDF

10:15-11:00: Whole genome sequencing methods and the raw data

Readings: Loman et al 2012 (Overview of whole genome sequencing methods) PDF

Slides: PDF

11:15-11:30: Coffee

11:30-12:15: Assembly and quality measures

Slides: PDF

12:15-13:00: Lunch

13:00-13:45: Intro to single-isolates, single CGE services

Readings: The CGE tool box (book chapter describing the 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 paper) PDF

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

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

Slides: PDF

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

Exercise1

15:00-15:15: Coffee break

15:15-15:30: Wrap-up of computerwork

Slides: PDF

15:30-15:45: Intro to group exercises

Readings: Harris et al 2013 (MRSA in hospital ward) PDF

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

Slides: PDF

15:45-17:00: Group exercises: Computer work w. data from Harris et al 2013 and Grad et al 2012

Exercise2