Oct 17 Workshopday3

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)


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.

Thanks for now and have a safe trip home!