In this course, we will cover algorithms for genomics, from genome assembly to pangenomics. The focus will be on the core concepts, algorithms and data structures underlying foundational and state-of-the-art methods, but also applications and future trends will be discussed. We will also practice implementation and discuss implementations. The course offers an engaging mix of lectures, paper discussions, hands-on exercises, and a small project.
Co-organisers
This course is organized by the BioSB research school in collaboration with Wageningen University and TU Delft.
Course coordinators
- Sandra Smit, Wageningen University
- Jasmijn Baaijens, TU Delft
Course credits
The study load of this course is 1.5 ECTS credits. Participants will get a certificate after successfully completing this course.
Course description
Comparative genomics entails the comparison of large sets of genomes, aiming to understand and explain differences in traits of an organism. Contemporary methods are powered by fundamental algorithms and data structures, which are efficient and scale to large data sets. A thorough understanding of these algorithms and data structures is necessary for advanced users and developers in this area. In addition, understanding how the field of comparative genomics is developing is important to shape your own research.
In this course, we will cover algorithms for genomics, from genome assembly to pangenomics. The focus will be on the core concepts, algorithms and data structures underlying foundational and state-of-the-art methods, but also applications and future trends will be discussed. We will also practice implementation and discuss implementations. The course offers an engaging mix of lectures, paper discussions, and hands-on exercises. It includes a project in which small groups will study a methods paper and its implementation in-depth, possibly including your own (partial) implementation, and present it to the other participants.
Learning objectives
After having followed this course, the student has a broad overview of relevant algorithms and data structures in comparative genomics, can understand algorithm descriptions (from bioinformatics papers) and their implementations, and gained some experience is able to implement algorithms in Python.
Target audience
The course is aimed at PhD students with a background in bioinformatics, computer science or a related field. Participants are expected to have experience in command-line usage (Unix shell) and programming (Python) and have basic knowledge of genomics.
Participants are expected to bring their own laptop.
Lecturers
- Sandra Smit, Wageningen University & Research
- Jasmijn Baaijens, TU Delft
- Anne Kubczok, Wageningen University & Research
- Rens Homer, Wageningen University & Research
Course program
General outline of the course (subject to changes depending on teacher availability):
Monday and Tuesday: Genome assembly
Wednesday: Alignment and variant calling
Thursday: Pangenomics
Friday: Guest lectures and project presentations
Overall structure of the course days (variations per day will occur):
09:00-10:00 Lecture
10:00-10:30 Coffee break
11:00-12:00 Exercises (e.g. implementation, code review, project work)
12:00-13:30 Lunch break
13:30-14:15 Lecture
14:15-15:00 Exercises (e.g. implementation, code review, project work)
15:00-15:30 Coffee break
15:30-16:30 Lecture or activity (e.g. project work or paper discussion)
Additional information
Software used: Python3
For more information about the course, you can contact dr. Sandra Smit
Wildcards
If you would like to join this course using a wildcard please contact the community manager.
Until the maximum number of wildcard spots is reached, you can register with a wildcard until September 1, 2025.
Always mention in your application from which academic group the wildcard comes. Your registration is only valid after confirmation from the community manager.
Registration
- € 480 (excl. VAT) for PhD/MSc students
- € 720 (excl. VAT) for academic researchers (non-profit)
- € 1080 (excl. VAT) industry participants (for profit)
Registration will close on 4 October 2025.
Course fees includes course materials and catering (coffee, tea and lunch)
You can register for the course by filling out this registration form
Find general enrollment information here.
