Home Pre-workhop Instructions
Lectures
1: Introduction and Key Concepts 2: Variant Detection and Phylogenetic Trees 3: Practical Applications of WGS and Phylogenetics 4: Advanced Applications of WGS
Practical 1: WGS Data Analysis
Obtaining sequencing data Viewing raw sequencing data QC of FASTQ files Cleaning and filtering FASTQs Reference mapping/alignment De novo assembly
Practical 2: Variant Calling and ML Trees
Variant calling and VCFs Building consensus sequences Aligning consensus sequences Maximum Likelihood trees
Practical 3: Timed Phylogenetic Trees
ML timed trees Bayesian trees (BactDating) Bayesian trees (BEAST2)
Practical 4: Transmission and Profiling
Identifying lineages and serotypes Transmission network reconstruction
Practical 5: Mixed Infection, Recombination and ANI
Identifying mixed infection Detecting recombination Average nucleotide identity (ANI)
Practical 6: Phylogeography and Phylodynamics
Phylogeography Inferring population dynamics
Practical 7: Fitness and Selection
Local branching index (LBI) Detecing homoplasy dN/dS GWAS


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Pre-workshop Instructions

Please click the link below for instructions to download and install all data and software required for this course:

Pre-workshop Instructions


Programme

Date Time Session Modules
Saturday 3rd May 9:30–10:30 Lecture 1: Introduction and Key Concepts • Course outline
• Introduction to next generation sequencing and genomic epidemiology
10:40–12:40 Practical Session 1: Whole Genome Sequence Data Analysis • Obtaining sequencing data
• Data manipulation and QC
• Reference-based mapping and de novo assembly
12:40–13:40 Lunch Break
13:40–14:15 Practical Session 1 (cont.): Whole Genome Sequence Data Analysis • Catch-up, overview, QA
14:15–15:15 Lecture 2: Variant Detection and Phylogenetic Trees • What is a variant? How do we call variants?
• Variant calling software and QC
• What are phylogenetic trees?
• Types of phylogenies, phylogenetic uncertainty (bootstrapping etc.)
15:30–18:00 Practical Session 2: Variant Calling and Maximum Likelihood Trees • Variant calling
• SNP filtering and QC
• Building SNP matrices
• Aligning consensus sequences
• Producing ML trees
Sunday 4th May 9:30–11:00 Lecture 3: Practical Applications of WGS and Phylogenetics • Species identification
• Resistance and plasmid profiling
• Transmission
11:00–12:00 Practical Session 3: Timed Phylogenetic Trees • One-step timed phylogenetic tree with BEAST2
• Two-step timed phylogenies using ML + Bayesian frameworks
12:00–13:00 Lunch Break
13:00–14:30 Practical Session 3 (cont.): Timed Phylogenetic Trees • (cont.) One-step timed phylogenetic tree
• Two-step timed phylogenies using ML + Bayesian frameworks
14:45–16:45 Practical Session 4: Transmission and Profiling • Identifying species, serotypes, and lineages from WGS
• Inferring transmission networks/clusters
16:45–17:00 Closing Remarks - Short Course • Short course summary and feedback collection
Monday 5th May (Advanced) 9:00–10:30 Lecture 4: Advanced Applications of WGS • Phylogeography and phylodynamics
• Recombination
• Average Nucleotide Identity (ANI)
• Mixed infection
• Fitness and selection
10:45–12:00 Practical Session 5: Mixed Infection, Recombination and ANI • Identifying mixed infection
• Calculating ANI
• Testing for recombination
12:00–13:00 Lunch Break
13:00–13:30 Practical Session 5 (cont.): Mixed infection, Recombination and ANI • (cont.) Identifying mixed infection
• Calculating ANI
• Testing for recombination
13:30–15:00 Practical Session 6: Phylogeography and Phylodynamics • Phylogeography (ancestral state reconstruction)
• Phylodynamic analysis with BEAST2 (Skyline analysis)
Tuesday 6th May (Advanced) 9:00–12:00 Practical Session 7: Fitness and Selection • Strain-specific fitness (LBI)
• Site-specific selection (homoplasy, dN/dS)
• GWAS
12:00–12:30 Closing Remarks - Advanced Course • Full course summary and feedback collection

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