Advanced workshop day1

8:30-9:00: Registration and light breakfast

9:00-9:30: Workshop and participants introduction

Readings: Quainoo et al 2017 (WGS is the future of nosocomial outbreak analysis) PDF

Slides: PDF

9:30-9:45: Introduction to working command line

Slides: PDF

Readings: Overview of Unix commands used throughout exercises PDF

9:45-10:15: 

Exercise1

Note: Output files for all exercises can be downloaded HERE.

10:15-10:30: Ex. 1 recap

Slides: PDF

10:30-10:45: Coffee

10:45-11:00: Amazon Web Services (AWS) - Cloud computing

Slides: PDF

11:00-11:15: Linux software installation

Slides: PDF

Readings: Overview of software used throughout exercises PDF

11:15-12:00: 

Exercise2

Note: Output files for all exercises can be downloaded HERE.

12:00-13:00: Lunch

13:00-13:30: Short read quality assessment and trimming 

Readings: Fabbro et al 2013 (Evaluating read trimming effects): PDF

Readings: FastQC documentation is available online HERE.

Readings: Cutadapt user guide is available online HERE.

Readings: Trimmomatic user guide is available online HERE.

Slides: PDF

13:30-14:45: 

Exercise3

Note: Output files for all exercises can be downloaded HERE.

Tutorial: Read trimming with Trimmomatic: PDF

Tutorial: Read trimming with Prinseq: PDF

14:45-15:00: Ex. 3 recap

Slides: PDF

15:00-15:15: Coffee

15:15-15:30: Assembly and draft genome quality assessment

Readings: Bankevich et al 2012 (SPAdes genome assembly) PDF

Readings: Li et al 2016 (Minimap/miniasm) PDF

Readings: Vaser et al 2017 (Racon) PDF

15:30-16:45: 

Exercise 4

Note: Output files for all exercises can be downloaded HERE.

16:45-17:00: Ex. 4 recap