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:
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:
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:
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:
Note: Output files for all exercises can be downloaded HERE.
16:45-17:00: Ex. 4 recap