Wellcome Connecting Science Course Run Website
Course Time Table 2025
Course Informatics Guide
Cite the course here:
K-mers are a powerful tool in bioinformatics, unlocking solutions to a wide range of genomics challenges. This workshop is designed to make k-mer-based methods accessible and practical for researchers at all levels, providing the skills and knowledge needed to harness these techniques in genomics research.
Presented by leaders in the field, participants will explore the core concepts of k-mers, learn to use essential tools, and gain insights into customising approaches for their unique research needs. With a focus on real-world applications, the workshop highlights how k-mers are particularly valuable for addressing questions in species lacking comprehensive reference genomes and annotations. Through interactive sessions utilising real-world case studies, attendees will see the transformative potential of k-mers in advancing their work.
By the end of the workshop, participants will have the knowledge and skills to confidently leverage k-mers for their genomics research.
This course is suitable for anyone that works with non-model organisms that wants to gain or strengthen their ability to analyse genomic data with custom pipelines. Familiarity with command line (bash, UNIX) and previous experience with genomics data is highly recommended.
After attending the course participants will be able to:
- Describe the concept of k-mers and the range of their utilities
- Apply several generic k-mer tools
- Evaluate quality of sequencing runs using k-mer spectrum
- Create genome profiling models to predict genomic features
- Apply k-mer logic to custom and out of box problems
The course will start on Sunday 1 June, in the afternoon with introductions and a computer setup check. Course sessions will run Monday to Friday, 09:00–17:30 (BST).
Monday to Thursday: Daily activities will include lectures, seminars, practical exercises, and networking activities to build knowledge and skills. The learning materials will cover the following topics:
- k-mers as a concept
- how k-mers can be counted efficiently and manipulated to compare samples or species
- k-mers for QCing whole genome sequencing libraries
- Genome profiling – estimating sequencing coverage, genome size, heterozygosity and ploidy using k-mers
- Working with k-mer indexes and graph representations of large sequencing datasets
Friday: A hackathon to provide an opportunity to apply these knowledge and skills by analysing participant’s own data or working with test datasets.
Course Instructors
- Eugene Myers, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan; Tree of Life, Wellcome Sanger Institute
- Rayan Chikhi, Institut Pasteur in Paris, France
- Katharine Jenike, University of Cambridge, Cambridge, UK
- Kamil S. Jaron, Tree of Life, Wellcome Sanger Institute
- Tessa Pierce-Ward, University of California, Davis, USA
Wellcome Connecting Science Team
- Michelle Bishop, Associate Director of Learning and Training at Wellcome Connecting Science
- Alice Matimba, Head of Training
- Mel Sharpe, Systems and Processes Manager
- Martin Aslett, Informatics Manager
- Vaishnavi Vikas Gangadhar, Informatics Technical Officer
The course data are free to reuse and adapt with appropriate attribution. All course data in these repositories are licensed under the Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0).
Each course landing page is assigned a DOI via Zenodo, providing a stable and citable reference. These DOIs can be found on the respective course landing pages and can be included in CVs or research publications, offering a professional record of the course contributions.
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