Mar17 workshop day 1

9:00-9:30: Registration and breakfast

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

Slides: PDF

10:00-10:15: 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

Slides: PDF

10:15-10:45: Illumina Next-Generation Sequencing for Microbiology (Pernille Albertus, Illumina Inc.)

Slides: PDF

10:45-11:00: Coffee

11:00-12:00: Sequencing techniques, the raw data, assembly, and quality measures

Multiple choice questions (for self-evaluation during lecture) PDF

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

Readings: Bleidorn 2016 (Third generation sequencing) PDF

Readings: Jünemann et al 2014 (Comparing assemblers) PDF

Slides: PDF

Instructions: Read trimming using PRINSEQ PDF

12:00-13:00: Lunch

13:00-13:45: 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 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 Exercise 2

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

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

Recap of Grad et al 2012 findings that we will refind PDF

Slides: PDF

15:45-17:00: Exercise 2: Computer work w. data from Harris et al 2013 and Grad et al 2012

Exercise2