Description

Next-generation sequencing (NGS) technologies have revolutionized many fields in biology and are changing the practice of medicine. As a joint state-of-the-art research and training facility of the ETH and the University of Zurich, the Functional Genomics Center Zurich (FGCZ) offers a course with hands-on practicals. The aim is to help scientists interested in NGS technologies, particularly applied to DNA sequencing, to gain a better understanding of the techniques available and their applications. This course is not meant to replace any manufacturers’ training normally supplied with an instrument.

The practical consists of a library preparation for short and long read technology starting from genomic DNA, followed by a sequencing run on a bench top sequencer. An introduction to the analyses of the resulting data and some exercises will be offered too. The lectures cover existing and upcoming NGS technologies, their applications and the principles of downstream data analysis.

The data analysis part starts off from the raw reads, as generated by the instrument, and cover pre-processing, alignment, variant calling and several quality control checkpoints. The hands-on sessions for data analysis do neither require a pre-existing knowledge of Unix nor the command line environment. This course is not intended to be a training course for those solely interested in next-generation sequencing bioinformatics.

By the end of the course participants should be able to make informed decisions about which technology and workflow to apply to solve specific research questions.

Course program

Library Prep
- DNA library generation: principles and types for long and short read NGS

Sequencing
- Detailed description of available sequencing technologies platforms
- Hands-on laboratory work: preparing and performing sequencing runs

Data analysis
- Run QC: Criteria for run performance
- Read QC: Metrics for evaluating short and long read quality
- Preprocessing of raw data
- Mapping reads to a reference genome
- Mapping QC: Metrics for mapping of DNA-seq reads
- Variant calling
- Visualisation of mapping and variant calling results
- De novo assembly steps
- IT and awareness of the data storage and its size