Advanced workshop day2

8:30-9:00: Light breakfast

9:00-9:15: Welcome back and intro

9:15-9:45: Read mapping to identify contaminating reads, and SNPs

Readings: PDF

Slides: PDF


Exercise 5

10:30-10:45: Coffee


Exercise 5 cont.

11:30-11:45: Ex. 5 recap

Slides: PDF

11:45-12:00: Introduction to PATRIC - Examining identified SNPs

Slides: PDF

12:00-13:00: Lunch

13:00-13:15: CGE databases and methods run commandline

Readings: Larsen et al 2012 (MLST paper) PDF

Readings: Carattoli et al 2014 (PlasmidFinder and pMLST paper) PDF

Readings: Larsen et al 2014 (KmerFinder paper) PDF

Readings: Roer et al 2017 (FimTyper paper) PDF

Readings: Zankari et al 2017 (PointFinder paper; identification of point mutations in chromosomal genes causing antimicrobial resistance PDF

Readings: Zankari et al 2012 (ResFinder paper; identification of acquired antimicrobial resistance genes) PDF

Readings: Joensen et al 2015 (SerotypeFinder paper) PDF

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

13:15-13:30: Docker - software in containers

Readings: PDF

Slides: PDF


Exercise 6

14:45-15:00: Ex. 6 recap

Slides: PDF

15:00-15:15: Coffee

15:15-15:30: Intro to NDtree


Exercise 7

16:15-16:30: Ex. 7 recap

16:30-17:00: Evaluation and workshop end