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:
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:
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:
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