Overview

Next-generation sequencing (NGS) has revolutionized genetic and genomic analysis, making it imperative for experimental scientists to acquire bioinformatics skills to analyze the vast amounts of data generated. This Course is designed to provide participants with the necessary informatics skills to analyze NGS data, focusing on human variant calling using high-performance computing (HPC). The program will cover prominent NGS technologies and the algorithmic theory behind bioinformatics analysis, emphasizing practical computational sessions using tools and resources applicable to human whole genome sequence data analysis. Participants will gain hands-on experience in QC, alignment, assembly and variant calling.

Skill level of training

Intermediate

Language

English

Credential awarded

Letter of completion

Type of training

Workshop

Venue

Online on Zoom

Course date

Every Tuesday and Thursday from 10:30 CAT to 14:30 CAT.

Notification date for successful applicants

Monday 27th of January 2025

Organisers

Anwani Siwada, Tshinakaho Malesa, Gerrit Botha, Shaun Aron, Sumir Panji, Scott Hazelhurst, Nicola Mulder

Sponsors

eLwazi Open Data Science Platform

Intended Audience

This course is aimed at postgraduate students and researchers who are working on projects that will need to do calling of variants from human whole genome sequence data in African populations.

Selection criteria / process

This will be a competitive selection process with preference given to applicants who are currently working with human whole genome sequencing data.

Prerequisites

• Currently working on or will soon be working on whole genome sequencing data, particularly wanting to perform variant calling
• Have foundational linux knowledge

Learning outcomes

After this course participants should be able to:

• Navigate the Unix command line and understand basic commands.
• Appreciate the benefits of using workflows for scientific reproducibility.
• Compare containerization technologies and understand their respective advantages.
• Identify common NGS platforms and describe their applications in research.
• Perform quality control on NGS data using FastQC and trimming/filtering techniques.
• Interpret alignment outputs and improve alignments for downstream analysis.
• Recognize different types of variants and understand variant calling approaches.
• Apply filtering techniques to VCF/BCF files and extract relevant information.
• Execute workflows and handle multiple samples for joint calling.
• Use downstream analysis tools for filtering VCF annotations and plan for future support.

Limitations

This course will only be limited to the stated learning outcomes and will not teach any advanced NGS data analysis skills.

To apply, please Click Here