Genomic Epidemiology of SARS-CoV-2 (Command Line)
Complete Training Course
Overview: The purpose of this course is to provide an overview of pathogen genomic epidemiology, followed by step-by-step instruction for laboratory preparation of SARS-CoV-2 sequencing libraries, bioinformatic assembly of SARS-CoV-2 genomes, and phylogenetic analysis. This course introduces the Linux command line, which is used for all bioinformatics analyses.
Prerequisites: Viral RNA extraction, basic lab technique with micropipettes, PCR amplification. Experience with the Linux command line is useful but not required.
Materials: Equipment and reagents needed to follow SARS-CoV-2 sequencing protocol are available here.
Syllabus: Example syllabus available here. All course materials are linked in the syllabus document.
Training modules
Module 1: Introduction to Pathogen Sequencing
Category: Theory. Language: English (with French subtitles). Runtime: 14 minutes
Module 2: Introduction to Genomic Epidemiology
Category: Theory. Language: English (with French subtitles). Runtime: 10 minutes
Module 3-1: Laboratory Methods for Pathogen Sequencing
Materials: Reagents & Equipment List, SARS-CoV-2 Sequencing Protocol, Library Preparation Worksheet
Category: Laboratory. Language: English (with French subtitles). Runtime: 14 minutes.
Module 3-2: Fluorometric DNA Quantitation
Materials: SARS-CoV-2 Sequencing Protocol (Instructions for quantification with Qubit Fluorometer in Appendix)
Category: Laboratory. Language: English (with French subtitles). Runtime: 10 minutes.
Module 4-1: Setting Up a MinION Sequencing Run
Category: Laboratory. Language: English (with French subtitles). Runtime: 15 minutes.
Module 4-2: Loading the MinION Sequencer
Category: Laboratory. Language: English (with French subtitles). Runtime: 8 minutes.
Module 5: Introduction to Sequencing Bioinformatics
Category: Bioinformatics. Language: English (with French subtitles). Runtime: 15 minutes.
Module 6-1: Introduction to the Command Line
Materials: Command Line Practice
Category: Bioinformatics. Language: English (with French subtitles). Runtime: 18 minutes.
Module 6-2: Running the SARS-CoV-2 Assembly Pipeline
Materials: Genome Assembly Protocol (and quick reference guide), File Paths Worksheet
Supplemental Materials: Software installation script, Sample SARS-CoV-2 sequencing data
Category: Bioinformatics. Language: English (with French subtitles). Runtime: 14 minutes.
Module 7: Manipulating Sequence Data
Materials: Genome Analysis Protocol, File Paths Worksheet
Supplemental Materials: Software installation script, Sample SARS-CoV-2 sequencing data
Category: Phylogenetics. Language: English (with French subtitles). Runtime: 11 minutes.
Module 8: Multiple Sequence Alignments
Materials: Genome Analysis Protocol, File Paths Worksheet
Supplemental Materials: Software installation script, Sample SARS-CoV-2 sequencing data
Category: Phylogenetics. Language: English (with French subtitles). Runtime: 9 minutes.
Module 9: Phylogenetic Trees
Materials: Genome Analysis Protocol, File Paths Worksheet
Supplemental Materials: Software installation script, Sample SARS-CoV-2 sequencing data
Category: Phylogenetics. Language: English (with French subtitles). Runtime: 14 minutes.
