Sep18 workshop day 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: 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

10:00-10:30: Computer work w. VTEC (ResFinder, VirulenceFinder, SerotypeFinder, MyDBFinder)

Exercise2

Guide: Databases on BitBucket PDF

10:30-10:45: Coffee

10:45-11:00: Exercise 2 continued

11:00-11:15: Wrap-up of computer work

Slides: PDF

11:15-12:00: Whole genome based phylogeny

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

12:00-13:00: Lunch

13:00-13:15: Introduction to computer work

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

Slides: PDF

13:15-14:15: Computer work - phylogeny (NDtree and CSIPhylogeny)

Exercise3

14:15-14:30: Coffee

14:30-15:00: Exercise 3 continued 

15:00-15:15: Wrap-up of computer work

Slides: PDF

15:15-15:45: Alternative tools for phylogeny + Identification of unique core 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

15:45-16:30: Computer work on RUCS

Exercise 4

16:30-17:00: Wrap-up of computer work

Slides: PDF