General Topic: Comparative genomics with a focus on structural variation
When: 1-5 October 2018
Where: Berlin, FU University
Instructors:
Dr. Fritz J Sedlazeck (Assistant Professor at the Human Genome Sequencing Center at Baylor College of Medicine, USA)
Prof. Ingo Ebersberger (Professor for Applied Bioinformatics, Goethe University Frankfurt, Germany).
Overview
This course will introduce biologists and bioinformaticians into the field of comparative genomics. Different techniques will be introduced to identify single nucleotide polymorphism (SNP) and structural variations (SVs) as well as the annotation of these variations and the assessment for their functional impact.
Format
The course is structured in modules over five days. Each day will include an introductory lecture with class discussion of key concepts. The remainder of each day will consist of practical hands-on sessions. These sessions will involve a combination of both mirroring exercises with the instructor to demonstrate a skill as well as applying these skills on your own to complete individual exercises. After and during each exercise, interpretation of results will be discussed as a group.
TARGETED AUDIENCE & ASSUMED BACKGROUND
The course is aimed at researchers interested in learning how to compare genomes and what can be learned from genomic similarities as well as variations. It will include information useful for both beginners and more advanced users. We will start by introducing general concepts of comparative genomics. On this basis, we will then continue to describe all major analysis steps from the raw sequencing data via the identification of variations to an assessment of their impact on the phenotype.
Attendees should have a background in biology. There will be a mix of lectures and hands-on practical exercises using command line Linux. We will therefore dedicate one session to introduce basic and advanced Linux concepts for processing data on Amazon cloud (AWS). Attendees should have also some familiarity with genomic data such as that arising from NGS sequencing experiments.
LEARNING OUTCOMES
- Identification of SNPs and SVs using de novo genome assembly and read mapping strategies
- Assessment of strengths and weaknesses of the different DNA sequencing technologies, Illumina, Pacific Bioscience, Oxford Nanopore, for the detection of variations
- Strengths and pitfalls of de novo assembly and mapping approaches for comparative genomics
- Hands on experience of state of the art methods to compare multiple genomes
- Annotation of variations and comparative genomics analysis
Course website: https://www.physalia-courses.org/cou...hops/course34/