Hands-on introduction to NGS variant analysis

Trainer St├®phane Plaisance
BITS Courses TRAINING AT VIB

Goal

Using a full publicly available chromosome read-set from one of the 1000 genome samples:
  •  Perform a complete analysis workflow including QC, read mapping, read coverage analysis, and variant calling against the human reference genome.
  • Use command line and open source software to evaluate each step of a classical NGS variant workflow and feel the complexity of the task.
  • Compare the obtained results with gold standard public data.
  • Identify bottlenecks and identify possible downstream analyses.
The skills acquired during this session should allow reproduction of the workflow by participants using their own reads and a reasonably-sized personal computer.

Summary

This training gives an introduction to the use of popular NGS analysis software packages at the command line. It reviews several exchangeable tools and provide hints to evaluate quality and content of DNA-Seq data by a biologist.
 
This training does not cover all methods available today. It does not aim at bringing users to a professional NGS analyst level but provides enough information to allow biologists understand what DNA sequencing practically is and to communicate with NGS experts for more in-depth needs.

Prerequisites

Skills required to follow this training include basic knowledge of human genome structure and nomenclature, basic knowledge of Illumina NGS read structure, basic Linux command line understanding. People who lack knowledge of Illumina reads can follow the 'Introduction to the analysis of NGS data' training. People who have no experience with Linux command line can follow the 'Linux for bioinformatics' training? or the 'Introduction to the analysis of NGS data' training.

BITS provides 15 laptops for their training sessions. Depending on the number of participants (max 20), it might be that you have to share the laptop with one other participant but you can also choose to bring your own Linux laptop for this training session.

Schedule

See the TRAINING AT VIB website for a detailed schedule of this training.

Training material

Links

Scientific topics DNA
Target audience Life Science Researchers, PhD students, post-docs, beginner bioinformaticians