Content
Week 1 Fundamentals of viral sequencing
- Glossary
- Introduction
to viral genomes
- Learning
more about SARS-CoV-2 genome
- Why
viral genome sequencing is important
- How
to sequence using Illumina technology
- Why
was Nanopore sequencing used in the SARS-CoV-2 pandemic?
- Using
metagenomics to investigate infections
- What
is viral whole-genome sequencing
- Using
sequencing to investigate SARS-CoV-2
- SARS-CoV-2
sequencing workflow
- Why
you should collect metadata
- How
to handle primary samples
- Storing
high-quality samples
- What
happens to samples after sequencing
- Assessing the quality of nucleic acid
Week 2 Library preparation and sequencing
- How
to isolate good quality nucleic acids
- What
a targeted sequencing protocol
- How
SARS-CoV-2 primer sets were designed
- Producing
SARS-CoV-2 amplicons
- Checking
the quality of amplicons
- What
is a sequencing library and how is it prepared?
- Comparing
library preparation methods
- Illumina:
pooling samples and loading cartridges
- Nanopore:
pooling samples and loading flow cells
- How
SARS-CoV-2 has been sequenced around the world
- Comparing
manual and automated methodologies
- How
to avoid contamination
- Coordinating
human resources in a pandemic
- How
to plan ordering and tracking of reagents
- Legacies of the COVID-19 pandemic
Week 3 Sequencing analysis and interpretation
- What
are sequencing metrics
- Accessing
and using sequencing data
- How
to generate a consensus sequence
- User-friendly
tools for quality control
- Why
high-quality data is important
- What
are clades, lineages and variants?
- SARS-CoV-2
Variants
- Interpreting
Nextclade quality metrics
- Lineages
classification using Pangolin
- Introduction
to phylogenetics: tools and models
- How
to detect an outbreak
- Generating
public health reports
- How
to prevent sequencing and sampling bias
- Using
sequencing data to identify outbreaks in a hospital
- The
importance of sample and data consent
- Establishing
collaborations in a pandemic
- Challenges
and how to overcome them
- Resources
