README.md

MICROBIOL582/EPID582 - Molecular Epidemiology and Pathogen Genomics Winter 2025

Instructor(s): Evan Snitkin and Heather Blankenship

Description: Provide an overview of cutting-edge approaches for Microbial Genomic analysis, with a focus on their application in the emerging field of genomic epidemiology. Lectures will be reinforced with discussions and extensive hands-on training. Students will gain experience on the command-line and in performing downstream analysis and visualization in R.

Date: Winter Term 2025

Course Discipline: Epidemiology

Overview:

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Section - Working with sequence data at the command line

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Class 1 – Setting up Great Lakes account and Introduction to UNIX

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• Sign up for Great Lakes account
• Intro to Unix
• Navigating directory structure
• Data Carpentry: Introducing the Shell & Navigating Files and Directories

Class 2 – Sequence data formats

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• Using GREP for pattern matching

Class 3 – For loops and computing on multiple files

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• Using for loops to perform same actions on different files

Class 4 – Introduction to Great Lakes and HPC

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• Working with Files and Directories
• Setting up your compute environment
• Loading modules
• Submit a job to cluster
• Setting up Jupyter Notebook with Great Lakes Open OnDemand

Section - Generating sequence data and performing annotation

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Class 5 – Illumina sequencing data and QC

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• Quality Control using FastQC
• Quality Trimming using Trimmomatic

Class 6 – Genome assembly

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• Performing assembly on the cluster
• Assess assembly quality with Quast
• Aggregate and Assess dataset quality using multiQC

Class 7 – Genome annotation

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• Genome annotation using PROKKA
• Identify antibiotic resistance genes with AMRFinderPlus

Class 8 – Data download and genome comparison

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• Download datasets from NCBI using SRA toolkit
• Compare genomes using Mashtree
• Visualize data and overlay metadata using iTol

Class 9 – Reference based variant calling

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• Variant calling Pipeline
• Variant calling using SNIPPY
• Visualize BAM and VCF files in IGV(http://software.broadinstitute.org/software/igv/)

Section - Basic phylogenetic analysis

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Class 10 – Intro to RStudio

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• The RStudio Interface and setting up an RProject
• Creating variables, performing operations and applying functions
• Reading in and parsing a gff file
• Exploring the pan-genome matrix created by panaroo
• Plotting a heatmap of AMR genes from ARIBA

Class 11 – Basic phylogenetic analysis

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• Exploring the relationship between community- and healthcare-acquired MRSA using phylogenetic analysis
• Tracking the origin of an blaNDM ST147 Klebsiella pneumoniae outbreak using phylogenetic analysis

Class 12 – Recombination detection

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• Perform Whole genome alignment with Parsnp
• Phylogenetic analysis in APE
• Perform SNP density analysis to discern evidence of recombination
• Perform recombination filtering with Gubbins

Section - Hospital outbreak investigation

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Class 13 – Overview of genomic epidemiology

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Class 14 – Regional outbreaks

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• Investigating Regional transmission using Genomic data

Class 15 – Regional endemic spread

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• Analyze AAC paper in regentrans

Section - Applications in Public Health

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Class 16 – Privacy, Policy and Politics

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• Examine the impact of data QC on genetic distance distributions
• Identify putative transmission clusters and examine makeup

Class 17 – Viral Genomic Epidemiology

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• Perform root-to-tip analysis before and after data QC
• Construct dated tree
• Overlay geographic data on tree