Content
Week 1 - Introduction to viral genomics
- Glossary
- Frequently
asked questions
- SARS-CoV-2
replication cycle
- SARS-CoV-2
genomic landscape
- Overview
of genomic, sub-genomic and anti-genomic sequences
- Introduction
to sequencing methods
- How
is SARS-CoV-2 sequencing done?
- Amplicon-based
sequencing
- Overview
of different data formats
- What
is bioinformatics?
- Overview
of web-based bioinformatics analyses using Galaxy
- Importing
data onto Galaxy
- Processing
data on Galaxy
- Building
a workflow on Galaxy
- Using existing workflows on Galaxy
Week 2 - Exploring the pipelines available
- Garbage
in/Garbage out: importance of generating good data and cleaning
up
- Data
cleaning and quality contro
- FastQC
and MultiQC tools
- Assess
quality with FastQC
- Assembly
of SARS-CoV-2 genome and sequence alignment
- Assembly
tutorial
- Variant
calling and annotation
- Variant
calling tutoria
- Using
and interpreting Nextclade
- Signatures
of co-infection, recombination and contamination
- What
are clades, lineages and variants?
- Prediction
of minor variants and drug resistance
- Identification
of recombinants
- Introduction
to phylogenetics: tools and models
- Transmission
detection: travel-associated, hospital and community
transmission
- Tutorial
on phylogenetics
- Quality control in phylogenetics
Week
3 - Introduction to genomic epidemiology of COVID-19 * The
importance of sample and data consent
* Ethics
in data sharing
* Metadata:
standardisation and collection tools
* Ownership
of analyses tools and pipelines
* Best
practices for data sharing
* Data
quality metrics
* Pros
and cons of public databases for data sharing
* When
and why to obtain sequencing data
* How
and where to obtain the public data
* Challenges
and limitations of data sharing
* Best
practices for presenting your data
* Public
health reports and sharing
* Resources
