Mar18 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

9:15-10:00: VTEC diagnostics

Readings: Joensen et al 2014 (VirulenceFinder and NDtree paper) PDF

Readings: Joensen et al 2015 (SerotypeFinder paper) PDF

Slides: PDF

10:00-10:45: Computer work w. VTEC (VirulenceFinder, SerotypeFinder, MyDBFinder)

Exercise3

Guide: Databases on BitBucket PDF

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

Slides: PDF

13:45-14:30: Computer work - phylogeny (NDtree and CSIPhylogeny)

Exercise4

14:30-14:45: Coffee

14:45-15:15: Exercise 3 continued 

15:15-15:30: Wrap-up of computer work

Slides: PDF (extra discussion points)

15:30-16:00: Other 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

RUCS paper

Slides: PDF

16:00-16:45: Computer work on cgMLST and RUCS

Exercise 4

16:45-17:00: Wrap-up of computer work

19:00: Workshop dinner in the restaurant at Rungstedgård