Sep18 workshop day 3

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.