23-27 February 2026

To foster international participation, this course will be held online

General Topic: Comparative genomics with a focus on structural variation

This course introduces biologists and bioinformaticians to the field of comparative genomics. It covers a broad range of software tools and analysis workflows, spanning from assembling and annotating small eukaryotic genomes, through the identification of single nucleotide variants (SNVs) and structural variants (SVs) within populations, to assessing the likely functional impact of these variants in an evolutionary context.

The course is organized into modules spread over five days. Each day begins with an introductory lecture and a class discussion on key concepts. The remainder of the day is dedicated to practical, hands-on sessions. These include instructor-led demonstration exercises where participants mirror the skills being taught, followed by individual exercises where participants apply these skills independently. Throughout and after each exercise, results are interpreted and discussed collectively as a group. We encourage participants to bring their own data to analyze and discuss during the course, whenever possible.

This course is designed for researchers interested in learning how to compare genomes and understand what genomic similarities and variations can reveal. It caters to both beginners and more advanced users. We will begin by introducing the general concepts of comparative genomics and then cover the major analysis steps—from raw sequencing data, through variant identification, to assessing their potential impact on phenotype.

Attendees should have a background in biology. The course combines lectures with hands-on practical exercises using the Linux command line. Therefore, we will dedicate a session to introduce basic and advanced Linux concepts for processing data on the Amazon cloud (AWS). Some familiarity with genomic data, such as that generated by next-generation sequencing (NGS) experiments, is recommended.

• Identification of SNPs and structural variants (SVs) using both de novo genome assembly and read mapping strategies

• Assessment of the strengths and weaknesses of different DNA sequencing technologies—Illumina, Pacific Biosciences, Oxford Nanopore—for variant detection

• Understanding the strengths and pitfalls of de novo assembly and mapping approaches in comparative genomics

• Hands-on experience with state-of-the-art methods for comparing multiple genomes

• Annotation of variants and conducting comparative genomics analyses

• Familiarity with biological sequence analysis in an evolutionary context

Monday: The Basics of Genome Scale Analyses - 2-8 PM Berlin time

Lecture 1:

• General introduction

• File formats: FastQ, SAM, BAM, GFF3

• Introduction to de novo assembly strategies, best practices, and quality control

Lab 1:

• Setting up computers / AWS instances

• Reads quality control (QC) and trimming

• Initial genome assembly steps

Tuesday: De novo Genome Assembly - 2-8 PM Berlin time

Lecture 2:

• De novo assembly continued: discussion and next steps

Lab 2:

• Run your own de novo genome assembly (short and long reads)

• Compute and interpret assembly summary statistics

Wednesday: Genome Annotation and Gene Set Completeness - 2-8 PM Berlin time

Lecture 3:

• Annotation of eukaryotic genomes

  • Repeat annotation

  • Gene identification

  • Gene order and shared synteny

Lab 3:

• Genome annotation using Maker2 pipeline

• Set up genome browser (IGV)

• Gene set completeness analysis

• Shared synteny analysis

Thursday: Comparative Genomics – Multi-Sample Structural Variant (SV) Comparison - 2-8 PM Berlin time

Lecture 4:

• What are SVs and their importance?

• Read mapping as the basis of SV calling

• Concepts and methods of SV calling

Lab 4:

• Choosing appropriate short-read mappers

• SV calling using de novo and mapping approaches

• Compare de novo and mapping-based SV results

• SV quality control

Friday: Predicting Functional Consequences of Genomic Variations - 2-8 PM Berlin time

Lecture 5:

• Gene function assessment (e.g., GO analysis)

• Functional changes due to loss, SVs, cis-regulation

• Impact on pathways (e.g., KEGG)

Lab 5:

• Functional annotation of variants

• Identification of orthologs/homologs across species

• GO annotation and analysis

• Running pathway analysis

Lecture 6:

• Summary and discussion

"I'd like to thank Fritz and Ingo for their time, really great instructors. And Fritz's bursts of comedy gold were highly appreciated too!"

"Great course - thanks to you all"

1-  Genome Assembly and Annotation - ONLINE, 9-13 March

2-Computational Pangenomics - ONLINE, 13-16 April