9:00-9:15: Welcome back and intro
Multiple choice questions for recap of yesterday's topics (for self-evaluation): PDF
Slides: PDF
9:15-9:30: The Bacterial Analysis Pipeline and batch upload
Readings: Thomsen et al 2016 (Pipeline paper) PDF
Slides: PDF
9:30-10:15: Computer work (batch upload, pipeline)
10:15-10:30: Coffee
10:30-11:00: Exercise 5 continued
11:00-11:15: Wrap-up of computer work
Slides: PDF
11:15-12:00: Metagenomics
Readings: Hasman et al 2014 (Urine metagenomics) PDF
Readings: Nordahl Pedersen et al 2015 (Airtoilet waste paper) PDF
Readings: Nordahl Pedersen et al 2017 (MGMapper paper) PDF
Readings: Simner et al 2017 (Promises and hurdles of metagenomics)PDF
Slides: PDF
12:00-13:00: Lunch
13:00-14:00: Computer work - MGMapper
14:00-14:15: Coffee
14:15-14:30: Wrap-up of computer work
Slides: PDF
14:30-15:00: Metagenome binning
Readings: Villarroel et al 2017 (PYO phage cocktails) PDF
Slides: PDF
15:00-15:30: CGE, the Global Microbial Initiative and Real World Applications
Readings: Hammerum et al 2015 (spread of NDM-1) PDF
Readings: Hammerum et al 2017 (vanA E. faecium) PDF
Slides: PDF
15:30-15:45: Evaluation and workshop ends
Please remember to pick up your course certificate before you leave.