9:00-9:15: Welcome back and intro
Multiple choice questions for recap of yesterday's topics (for self-evaluation): PDF
Slides: PDF
9:15-9:45: The Bacterial Analysis Pipeline and batch upload
Readings: Thomsen et al 2016 (Pipeline paper) PDF
Slides: PDF
9:45-10:45: Computer work (batch upload, pipeline)
10:45-11:00: Coffee
11:00-11:15: Wrap-up of computer work
Slides: PDF
11:15-12:00: CGE and The Global Microbial Identifier Initiative (Ole Lund, DTU)
Slides:
12:00-13:00: Lunch
13:00-14:00: Real world applications (Henrik Hasman, SSI)
Readings: Hammerum et al 2015 (spread of NDM-1) PDF
Readings: Hammerum et al 2017 (vanA E. faecium) PDF
14:00-14:30: 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
Slides: PDF
14:30-14:45: Coffee
14:45-15:30: Computer work - MGMapper
15:30-15:45: Wrap-up of computer work
Slides: PDF
15:45-16:00: Evaluation and workshop ends
Please spend 5 minutes evaluating the workshop: Evaluation
Please remember to pick up your course certificate before you leave.