9:00-9:15: Welcome back and intro
Multiple choice questions for recap of yesterday's topics (for self-evaluation) PDF
Slides: PDF
9:15-10:00: E. coli diagnostics and the CGE databases
Readings: Zankari et al 2017 (PointFinder/ResFinder-3.0) PDF
Readings: Joensen et al 2015 (SerotypeFinder paper) PDF
Readings: Zhang et al 2015 (SeqSero paper) PDF
Readings: Thrane et al 2016 (PAst paper) PDF
Readings: Joensen et al 2014 (VirulenceFinder and NDtree paper) PDF
Readings: Grad et al 2012 (German E. coli outbreak) PDF
Slides: PDF
10:00-10:45: Computer work w. VTEC (VirulenceFinder, SerotypeFinder, MyDBFinder)
Guide: Databases on BitBucket PDF
10:45-11:00: Coffee
11:00-11:45: Exercise 2 continued
11:45-12:00: Wrap-up of computer work
Slides: PDF
12:00-13:00: Lunch
13:00-13:45: Whole genome based phylogeny (Johanne Ahrenfeldt)
Readings: Leekitcharoenphon et al 2014 (NDtree) PDF
Readings: Kaas et al 2014 (CSIPhylogeny) PDF
Readings: Ahrenfeldt et al 2017 (Constructing benchmarking set and assessing existing methods) PDF
Readings: Schürch et al 2018 (Species-specific SNP thresholds for outbreak detection) PDF
Slides: PDF TBA
13:45-14:00: Introduction to computer work
Readings: Harris et al 2013 (MRSA in hospital ward) PDF
Slides: PDF
14:00-14:30: Computer work - phylogeny (NDtree and CSIPhylogeny)
14:30-14:45: Coffee
14:45-15:15: Exercise 3 continued
15:15-15:30: Wrap-up of computer work
Slides: PDF
15:30-16:00: Alternative tools for phylogeny + Identification of unique cores sequences
Readings: Ruppitsch et al 2015 (Listeria cgMLST) PDF
Readings: Woksepp et al 2017 (value of cgMLST and SNP-based phylogeny) PDF
Readings: NCBI Pathogen Detection Factsheet PDF
Readings: Thomsen et al 2017 (RUCS paper) PDF
Slides: PDF
16:00-16:45: Computer work on RUCS
16:45-17:00: Wrap-up of computer work
Slides: PDF
18:30: Workshop dinner in the restaurant at Rungstedgård