Course overview
This course will provide training in laboratory and bioinformatics protocols for pathogen genomics, with a focus on SARS-CoV-2.
Instructors
- Darrell Dinwiddie
- Daryl Domman
Overview
- Week 1 : Introduction to Next-Generation Sequencing (Dinwiddie)
- Week 2 : Good Laboratory Practices for NGS Processes (Dinwiddie)
- Week 3 : Introduction to NGS Data and File types (Domman)
- Week 4 : Introduction to working on the command line and virtual machine (Domman)
- Week 5 : Illumina Library Prep and Sequencing (Dinwiddie)
- Week 6 : Illumina data QC and conda environments (Domman)
- Week 7 : Nanopore based SARS-CoV-2 genome sequencing protocols (Dinwiddie)
- Week 8 : Mapping (Domman)
- Week 9 : General pathogen sequencing protocols (Dinwiddie)
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- Week 10 : Bacterial Genome Assembly and Annotation (Domman)
- Week 11 : Comparison of Sequencing Technologies for Pathogen Sequencing (Dinwiddie)
- Week 12 : SARS-CoV-2 pipeline (Domman)
- Week 13 : Nanopore troubleshooting, common mistakes & solutions (Dinwiddie)
- Week 14 : SARS-CoV-2 lineage calling and phylogeny (Domman)
Virtual Machine Setup Guide
Module 1 - Intro to NGS data
Module 2 - Intro to Command Line