NGS - Genome Variant analysis - Sequencing and alignment (2 of 5)

The video was recorded live during the SIB course “NGS - Genome Variant analysis” streamed on 05-06 September 2023.
Target audience: This course is intended for life scientists who are already familiar with general concepts of NGS technologies and want to expand their knowledge and skills on variant analysis.
Speaker: Dr. Geert van Geest, SIB Swiss Institute of Bioinformatics
The course materials can be found in the dedicated GitHub page: sib-swiss.gith... .
Learning outcomes:
Describe the general workflow of library preparation and sequencing with an Illumina sequencer
Explain how the fastq format stores sequence and base quality information
Calculate probability from phred quality and the other way around
Explain why base quality and mapping quality are important for detecting variants
Illustrate the difference between short-read and long-read sequencing
Explain what impact long read sequencing can have on variant analysis
Describe how alignment information is stored in a sequence alignment (.sam) file
Define a duplicate alignment and explain how alignment duplicates can affect variant analysis
Any questions about this talk? Contact: Geert van Geest, [e-mail]
This video is available under the creative commons license CC-BY-4.0