This course offers a practical introduction to Pathogen Bioinformatics for Genomic Epidemiology, using both Galaxy and command line interface (CLI). It will use analysis of SARS-CoV-2 sequencing data as an example and also cover handling metadata to add context to the sequencing data being discussed and illustrate techniques in genomic epidemiology.
Programme
The course is a two week (10 days) programme of in-person instruction combining theoretical back with practical instruction and opporunity for hands-on practice of the skills presented.
| Week 1 | |||||
| Day 1 (Mon) | Day 2 (Tue) | Day 3 (Wed) | Day 4 (Thu) | Day 5 (Fri) | |
|---|---|---|---|---|---|
| 09h00 | Introduction to Sequencing and Genomic Epidemiology |
Metadata and data organisation -
Introduction to SARS-CoV-2 metadata organisation |
SARS-CoV-2 amplicon sequencing and primer schemes | Continue with Intro to SARS-CoV-2 Practical | Computing a phylogeny in Galaxy |
| 09h30 | Intro to SARS-CoV-2 analysis with Galaxy | Visualising phylogeny and metadata using Microreact | |||
| 11h00 | Tea Break | ||||
| 11h30 | Introduction to Galaxy 1 | Introduction to Galaxy 2 | Running Galaxy SARS-CoV-2 workflow | Intro to Phylogenomics | Hands on with phylogeny and Microreact |
| 13h00 | Lunch Break | ||||
| 14h00 | Introduction to Galaxy 1 Practical | Introduction to Galaxy 2 Practical | Galaxy SARS-CoV-2 Practical | Nextclade for SARS-CoV-2 + Practical | |
| Week 2 | |||||
| Day 6 (Mon) | Day 7 (Tue) | Day 8 (Wed) | Day 9 (Thu) | Day 10 (Fri) | |
|---|---|---|---|---|---|
| 09h00 | Intro to the Shell and Command Line | Setup of Software for Shell | Installing software with Conda and Mamba | Introduction to Nextflow | Building a workflow in Nextflow |
| 09h30 | Genomics in the Shell | SSH, SCP and Rsync | Nextflow workflow for SARS-CoV-2 | ||
| 11h00 | Tea Break | ||||
| 11h30 | Intro to the Shell | Genomics in the Shell | Manipulating tabular data with csvtk | Nextflow workflow for SARS-CoV-2 | Building a workflow in Nextflow |
| 13h00 | Lunch Break | ||||
| 14h00 | Intro to the Shell - Practical | Genomics in the Shell - Practical | Practical exercises | Nextflow practical exercises | Nextflow practical exercises |
Partners
This course is being organised by SANBI (the South African National Bioinformatics Institute) at the University of the Western Cape (UWC) in collaboration with Africa CDC (the Africa Centres for Disease Control and Prevention), part of the African Union (AU).
