12-16 February 2024

To foster international participation, this course will be held online

General Topic: Comparative genomics with a focus on structural variation

This course will introduce biologists and bioinformaticians into the field of comparative genomics. We will cover a broad range of software and analysis workflows that extend over the spectrum from assembling and annotating small eukaryotic genomes, via the identification of single nucleotide variants (SNVs) and structural variants (SVs) within the population, to the assessment of their likely functional impact of the detected variants in an evolutionary context.  

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.

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.

• 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
• Familiarity with biological sequence analysis in an evolutionary context

- We will use data from a fungal genome sequences project for the example analyses

- We encourage the participants to bring, analyze (if possible) and discuss their own data

Monday  – Classes from 2 to 8 pm Berlin time. The basics of genome scale analyses

Lecture 1

-       General introduction

-       File formats: FastQ, SAM, BAM, GFF3

-       Introduction in de novo assembly strategies, best practices and quality control

Lab 1

-       Setting up the computers/AWS instances

-       Reads QC + trimming

-       First steps in genome assembly