Course content

To see details about the live ‘Genome bioinformatics: from short- to long-read sequencing’ 2024 course and the original programme, you can refer to the course page and programme. Materials from previous editions of the course are available under request.

The contents table below outlines the different sessions that were included in the course, as well as the format of the materials (slides/videos/practicals) and each session’s trainer. Either proceed through the materials using the arrows at the end of each page or pick your topic of interest from the table below to skip straight to it.

 Presentation slides –  View or download the slides

 Recorded lectures – Watch the lecture videos 

 Practicals – View or download the slides, exercises, datasets, analysis scripts and results

Programme

Format	Subject	Trainer(s)
	Introduction to BASH, loops, and variables	Kayesha Coley
	NGS, raw read pre-processing, quality control, and read mapping
	Overview of NGS technology	Chiara Batini and Pille Hallast
	Quality control	Charles Solomon and Chiara Batini
	Read mapping	Charles Solomon and Chiara Batini
	Alignment and Genome assembly
	SAM/BAM file formats, BAM refinement, QC & visualisation	Chiara Batini
	Genome Assembly	Victor Flores Lopez
	Variant calling
	Introduction to Variant calling: SNPs and Indels	Raheleh Rahbari and Rashesh Sanghvi
	Variant calling and filtering through short-read sequencing (SNPs and indels) – practical	Raheleh Rahbari and Rashesh Sanghvi
	Variant calling: SVs & CNVs	Maxime Tarabachi
	Variant annotation and effect prediction
	Annotation and Variation with Ensembl	Jose Maria Gonzalez Perez-Silva and Sarah Hunt
	Ensembl ‘Variant Effect Predictor’ tutorial	Jorge Batista da Rocha
	Long-read sequencing	Mohab Helmy
	Pangenomics session	Erik Garrison
	Parallel processing and Pipeline building
	Scaling things up: Genome bioinformatics on clusters & parallel computing – lecture and practical	Sean Laidlaw
	Building a pipeline	Victor Flores Lopez
	Version control and Responsible Data management
	Introduction to GitHub	Sean Laidlaw
	Data management	Daniel Thomas López