Course: Algorithms for Genomics (1st edition)

Date & location

October 14-18, 2019

Location: Social Data Lab (0.E220), Van Mourik Broekmanweg 6, Delft

Course coordinators

  • dr. Thomas Abeel (TU Delft),
  • prof. dr. Alexander Schönhuth (CWI)
  • dr. Sandra Smit (Wageningen University)

Course credits

The study load of this course is 3 ECTS credits. Participants will get a certificate after successfully completing this course.

Course overview

Comparative genomics aims to compare large sets of genomes in order 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 comparative genomics is developing is important to shape your own research.      

In this course, we will cover genome analysis, variant analysis, and pangenomics. Core concepts, applications, and future trends will be discussed, with a focus on the algorithms and data structures underlying state-of-the-art methods. The course offers an engaging mix of lectures, paper discussions, hands-on tutorials, and a do-it-yourself project.

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.

Learning outcomes

After having followed this course, the student has a good understanding of algorithms and data structures in comparative genomics, is able to implement algorithms in python, is able to read and understand method papers in bioinformatics in detail, and is able to work with state-of-the-art command-line tools for genomics.


  • Preparation homework (paper reading)
  • Day 1: Genome assembly
  • Day 2: Mapping and variant calling/analysis
  • Day 3: Project
  • Day 4: Pangenomics
  • Day 5: Project and poster session

Daily time schedule

Day 1, 2, and 4:

  • 09:00-10:30 lectures
  • 10.30-11.00 coffee/tea break
  • 11.00-12.30 computer exercises
  • 12:30-13:30 lunch break
  • 13.30-15.00 computer exercises
  • 15.00-15.30 coffee/tea break
  • 15.30-17.30 literature discussion

Schedule day 3:

  • 9.00-12.30 project
  • 12.30-13.30 lunch break
  • 13.30-17.30 project

Schedule day 5:

  • 9.00-12.30 project + poster preparation
  • 12.30-13.30 lunch break
  • 13.30-15.00 poster preparation and printing
  • 15.00-17.00 poster session with drinks

More information

For more information about the course programme you can contact dr. Sandra Smit.


Maximum number of participants is 30, so register soon to be sure of a course seat! Registration is closed. You can contact if you have any questions. You can also pre-register for the next edition via this form.

The registration fees for this 5-day course are:

  • PhD student: 400 euro (excl. VAT)
  • Academic researcher (PI/Postdoc): 600 euro (excl. VAT)
  • Industry: 900 euros (excl.VAT)

The course fee includes:

  • Course material: Handouts, tutorials, required software will be made available online.
  • Catering: Coffee, tea and soft drinks and lunch will be provided.

You can register via the registration form