Bioinformatics for SARS Genomic Surveillance
Introduction
3
Bioinformatic workflows
Welcome
Overview
Data & Software
Introduction
1
SARS-CoV-2 genomic surveillance
2
Introduction to NGS
3
Bioinformatic workflows
Clinical Isolates
4
Consensus assembly
5
Quality Control
6
Lineages and variants
7
Building phylogenetic trees
Case Studies
8
Switzerland (Nanopore)
9
South Africa (Illumina)
10
EQA (Exercise)
Wastewater Samples
11
Wastewater Surveillance
12
Lineage Abundance
13
Abundance Visualisation
14
Mutation Analysis
Software
15
Managing Bioinformatics Software
16
Software setup
Appendices
Common file formats
Unix cheat sheet
R fundamentals
Tools and Resources
3
Bioinformatic workflows
Warning
Under development
2
Introduction to NGS
4
Consensus assembly