NGS Academy Bioinformatics Training on Pathogen Surveillance 2024

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Logistics:

Venue of course: South African National Bioinformatics Institute (SANBI), University of the Western Cape. Cape Town. South Africa
Hotel: Protea Hotel Tyger Valley Cape Town. South Africa (+27 21 913 2000)
Dates for the course: 4-15th March 2024 (2 weeks)
Training format: 2 Weeks in-person training
Contact Person: Tony Yiqun Li. NGS Academy team, Email: lxxyiq001@myuct.ac.za

Purpose of the course:

1. Develop fundamental bioinformatics skills, increasing programming knowledge and developing additional computational skills
2. Introduce different bioinformatic workflows for specific pathogen surveillance scenarios
3. Provide examples of workflows and analysis using Galaxy, and through coding in R.
4. Go through a use case of a cholera outbreak to teach bacterial pathogen surveillance.
5. Use case we look at the web tools, but focus on the command line with the Bactopia workflow (which is a well maintained nf-core compliant Nextflow workflow) and visualisation using Microreact and Grapetree.

Course prerequisites:
Intermediate coding skills in R, computer skills, using basic command lines. Knowledge around some workflow tools.

Intended audience:
Intermediate level bioinformaticians working with next-generation sequencing data for disease surveillance on the African continent.

Patner Institutions:

Week #1

Week One

Topic	Course materials	Training partner	Interactive Sessions with Instructor/s
Introduction Unix/linux, command line, shell scripting	1.1 Linux, unix, command line, Introduction to Shell, finding & working with files and directories, filters and pipes, loops, writing Shell scripts. Command line tools for genomic data. Videos Day 1 Morning Session Day 1 Afternoon Session	South African Bioinformatics Institute (SANBI)	Peter van Heusden

Topic	Course materials	Training partner	Interactive Sessions with Instructor/s
Introduction Unix/linux, command line, shell scripting cont...	2.1 Linux, unix, command line, Introduction to Shell, finding & working with files and directories, filters and pipes, loops, writing Shell scripts. Command line tools for genomic data. Videos Day 2 Morning Session 1 Day 2 Morning Session 2 Day 2 Afternoon Session	South African Bioinformatics Institute (SANBI)	Peter van Heusden

Topic	Course materials	Training partner	Interactive Sessions with Instructor/s
Package management with Conda	3.1.a Introduction to Conda 3.2 Coding fundamentals in Conda,, repeating actions with loops, command-line programs Videos Day 3 Morning Session 1 Day 3 Morning Session 2 Day 3 Morning Session 3 Day 3 Afternoon Session 1 Day 3 Afternoon Session 2	KEMRI-Wellcome Trust Research Programme	Dr George Githinji

Topic	Course materials	Training partner	Interactive Sessions with Instructor/s
Containers	4.1.a Introduction to containerisation 4.1.b Docker exercise 4.1.c Sequences.fasta 4.1.d primers.fasta 4.2 Containers workflow, theory, coding Videos Day 4 Morning Session 1 Day 4 Morning Session 2 Day 4 Afternoon Session 1 Day 4 Afternoon Session 2	KEMRI-Wellcome Trust Research Programme	Dr George Githinji

Topic	Course materials	Training partner	Interactive Sessions with Instructor/s
Nextflow workflows	5.1 Nextflow theory, coding	International Livestock Research Institute (ILRI)	John Juma

Week #2

Week Two

Topic	Course materials	Training partner	Interactive Sessions with Instructor/s
R programming	6.1 Introduction R and RStudio IDE, creating functions, R basics analysing multiple datasets R, factors and data frames, dplyr, data visualisation with ggplot2, best practices, producing reports, reading and writing CSV files, loops in R Videos Day 6 Morning Session 1 Day 6 Morning Session 2 Day 6 Afternoon Session 1	South African Bioinformatics Institute (SANBI)	Nasr

Topic	Course materials	Training partner	Interactive Sessions with Instructor/s
R programming cont...	7.1 Introduction R and RStudio IDE, creating functions, R basics analysing multiple datasets R, factors and data frames, dplyr, data visualisation with ggplot2, best practices, producing reports, reading and writing CSV files, loops in R Videos Day 7 Morning Session 1 Day 7 Morning Session 2 Day 7 Afternoon Session 1	South African Bioinformatics Institute (SANBI)	Nasr

Topic	Course materials	Training partner	Interactive Sessions with Instructor/s
Galaxy Introduction	8.1 Introduction R and RStudio IDE, creating functions, R basics analysing multiple datasets R, factors and data frames, dplyr, data visualisation with ggplot2, best practices, producing reports, reading and writing CSV files, loops in R Videos Day 8: Working on remote pc Day 8: Issues checking part 1, cholera case study Day 8: Issues checking part 2 Day 8: Morning Session 1 Day 8: Afternoon Session 1	South African Bioinformatics Institute (SANBI)	Tracey

Topic	Course materials	Training partner	Interactive Sessions with Instructor/s
Cholera case study	9.1 Cholera examples Videos Day 9 Morning session 1 Day 9 Morning Session 2 Day 9 Afternoon Session 1 Day 9 Afternoon Session 2	South African Bioinformatics Institute (SANBI)	Peter van Heusden

Topic	Course materials	Training partner	Interactive Sessions with Instructor/s
Cholera case study ... Additional work	10.1 Cholera examples cont... Videos Day 10 Morning session 1 Day 10 Morning Session 2 Day 10 Morning Session 3	South African Bioinformatics Institute (SANBI)	Peter van Heusden