8:30-9:00: Breakfast
9:00-9:15: Welcome back and intro
Multiple choice questions for recap of yesterday's topics (for self-evaluation) PDF
Slides: PDF
9:15-9:45: VTEC diagnostics
Readings: Joensen et al 2014 (VirulenceFinder and NDtree paper) PDF
Readings: Joensen et al 2015 (SerotypeFinder paper) PDF
Slides: PDF
9:45-11:00: Computer work w. VTEC (VirulenceFinder, SerotypeFinder, MyDBFinder)
11:00-11:15: Coffee
11:15-12:00: 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
Slides: PDF
12:00-13:00: Lunch
13:00-14:00: Computer work - phylogeny (NDtree and CSIPhylogeny)
14:00-15:00: Preparations of participant presentations
Ecoli1 group stays here (Template for presentation PDF )
Ecoli2 group goes to group room 3 (1st floor) (Template for presentation PDF )
MRSA1 group goes to group room 10 (1st floor) (Template for presentation PDF )
MRSA2 group sits in common area (e.g., at deck 1st floor) (Template for presentation PDF )
15:00-15:15: Coffee
15:15-16:15: Participant presentations and discussions
Ecoli1: PPTX
Ecoli2: PPTX
MRSA1: PPTX
MRSA2: PPTX
Slides: PDF (extra discussion points)
16:15-17:00: Alternative tools for typing and phylogeny
Readings: Zhang et al 2015 (SeqSero paper) PDF
Readings: Thrane et al 2016 (PAst paper) PDF
Readings: Ruppitsch et al 2015 (Listeria cgMLST) PDF
Slides: PDF
17:00: Bus pick-up
19:30: Workshop dinner at Club Riva, Rungsted Harbour