Oct 17 Workshopday 2

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)


Guide: Databases on BitBucket PDF

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 template for presentation PPTX

Ecoli2 group template for presentation PPTX

MRSA1 group template for presentation PPTX

MRSA2 group template for presentation PPTX


15:00-15:15: Coffee

15:15-16:15: Participant presentations and discussions

Ecoli1: PDF

Ecoli2: PDF



Slides: PDF (extra discussion points)

16:15-17:00: Other tools for typing and phylogeny

Readings: Zhang et al 2015 (SeqSero paper) PDF

Readings: Thrane et al 2016 (PAst paper) PDF

Readings: Zankari et al 2017 (PointFinder/ResFinder-3.0) PDF

Readings: Ruppitsch et al 2015 (Listeria cgMLST) PDF

Slides: PDF


19:00: Workshop dinner in the restaurant at Rungstedgård