Course content

To see details about the live ‘Genome bioinformatics: resequencing and variant calling’ course and the original programme, you can refer to the course page and programme.

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

FormatSubjectTrainer(s)
Raw read pre-processing, quality control, and read mapping
Overview of NGS technologyChiara Batini
Introduction to UnixKayesha Coley
Quality controlCharles Solomon
Read mappingCharles Solomon and Chiara Batini
Alignment
SAM/BAM file formatsChiara Batini
Introduction to BASH, loops, and variablesKayesha Coley
BAM refinement, QC & visualisationChiara Batini
Variant calling
Variant filteringChiara Batini
Variant calling and filteringChiara Batini
Variant calling SVs & CNVsMaxime Tarabachi and Raheleh Rahbari
Parallel processing, version control and open, reproducible science
Scaling things upSean Laidlaw and Raheleh Rahbari
Introduction to GitHubSean Laidlaw and Raheleh Rahbari
The Turing Way and reproducible research aspects of data scienceMalvika Sharan
EMBL-EBI resources for genomics and genomic inequity keynote
Ensembl genome browser & VEPAleena Mushtaq
Genomic inequity keynoteMarie Nugent and Samuel Tallman
European Nucleotide ArchiveMaira Ihsan
European Variation ArchiveBaron Koylass