Computational

K-mer Workshop for Biodiversity Genomics

1–6 June 2025

Wellcome Genome Campus, Hinxton

Introduction and advanced uses of k-mers in biodiversity genomics using modern k-mer tools and methods. 

Summary

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.

Who should attend this course?

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. 

Learning outcomes

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

Programme

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.

Organisers and speakers

Training Team & Organiser

  • 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
  • Kathrine Janike: University of Cambridge, Cambridge, UK
  • Kamil S. Jaron: Tree of Life, Wellcome Sanger Institute

 

How to apply

How to Apply

  1. Start the application
    • Click on the “Apply” button to start your application. Please note that places are limited and will be awarded based on merit.
  2. Demonstrate the course’s relevance to your project/role
    • Our courses are highly subscribed, so it is essential to clearly show how the skills you will learn in the course will be directly applicable and beneficial to your current role/project and how you plan to disseminate the knowledge after the course.
    • Preference will be given to applicants who are currently working on related projects or soon will be.
  3. Letter of recommendation

    • Applications must be supported by a recommendation from a scientific or clinical sponsor (e.g., supervisor, line manager, or head of department). Ensure that your sponsor provides a tailored supporting statement by the application deadline. This statement must be uploaded as a PDF document to the registration system within your application. Applications without a supporting statement will not be considered.
  4. Need help?
    • If you encounter any problems with the online application process, please contact us at courses@wellcomeconnectingscience.org for assistance.

Application deadline:  11 March 2025

Travel visas

Citizens of many countries can travel to the UK to attend a course or conference without needing a visa. Please check the UK government website for visitor information: https://www.gov.uk/standard-visitor.

Confirmed attendees requiring a letter to support a visa application should contact us courses@wellcomeconnectingscience.org.

Cost

Cost Accommodation / meals
*Course fee £ 1,062 includes accommodation and all meals

*The course fee is subsidised by Wellcome Connecting Science. Contact us at courses@wellcomeconnectingscience.org for the commercial rate.

The fee will be requested once acceptance is confirmed.

Bursaries

Limited bursaries are available (up to 50% reduction on the course fee) and are awarded on merit. If you would like to apply for a bursary, please complete the bursary section of the online application form, explaining why you would benefit from funding.

Bursaries can be applied for as part of the course application form. Applicants will be notified of a bursary award along with their place on the course, usually within one month of the application deadline. The decision of the selection committee is final.

Please note that both the applicant and sponsor are required to provide a justification for the bursary as part of the application.

Deadline: 11 March 2025

Additional funding opportunities
Visit our support page for additional financial support currently available.

Extra accommodation
If you wish to book onsite accommodation either side of the course dates, please contact Hinxton Hall Conference Centre directly.


Accommodation services phishing scam – please be vigilant. More information.

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