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: Li et al 2009 (BWA) PDF

Readings: Li et al 2009 (BWA-MEM) PDF

Readings: SAM format and Samtools (short version): PDF

Readings: SAM format (long version) can be found online HERE.

Readings: VCF format and VCFtools (short version): PDF

Readings: VCF format (long version) can be found online HERE.

Readings: PICARD documentation can be found online HERE.

Slides: PDF

9:45-10:30:  

Exercise 5

Note: Output files for all exercises can be downloaded HERE.

10:30-10:45: Coffee

10:45-11:30:  

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

13:00-13:30: CGE methods and databases + Docker

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

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

Tutorial: How to download the CGE databases and run the CGE methods via Docker: PDF

Slides: PDF

13:30-14:45:

Exercise 6

Note: Output files for all exercises can be downloaded HERE.

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

Slides: PDF

15:00-15:15: Coffee

15:15-15:30: Phylogenetic trees and NDtree

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

Slides: PDF

15:30-16:15:

Exercise 7

Note: Output files for all exercises can be downloaded HERE.

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

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