Scalable Genomics and Pangenomics

Genomics has moved beyond single reference genomes. Large-scale sequencing projects now investigate variation across populations and species, often involving hundreds or thousands of genomes. This expansion creates new opportunities to study structural variation, gene content diversity, and evolutionary processes, while demanding analytical approaches that remain efficient and robust at scale.

This course introduces the principles of scalable genomics and pangenomics, grounded in the core k-mer based concepts. Participants will explore genome profiling, k-mer spectra, and reference-free quality assessment to understand how sequence data can be efficiently summarised and compared. The programme then broadens to examine the limitations of linear reference genomes and to explore pangenome frameworks and graph-based representations as alternatives for modelling genomic diversity.

Across the week, the focus remains on linking biological questions to computational design. Beyond focusing on individual tools, the course examines scalable strategies for multi-genome comparison, data indexing, compression, and workflow planning. Real datasets and guided exercises to understand how performance considerations such as memory use and runtime influence interpretation at a scale.
By the end of the course, participants will have a clear conceptual of how k-mer based approaches integrate with pangenome models in modern genomics. They will be equipped to make informed methodological choices and to outline scalable analysis strategies aligned with their research goals.

Who should attend this course?

This course is designed for researchers working in population genomics, comparative genomics, evolutionary biology, or large-scale sequencing projects, particularly those studying non-model organisms. Participants should be familiar with the Linux or UNIX command line and have prior experience handling genomic data.

To support preparation, an optional six-hour introductory Linux module is available through our Learning Management System. Attendees must bring their own personal laptop and will be required to install a few software tools before the course.

By the end of the course, participants will be able to:

• Explain the core principles of scalable genomics and k-mer based analysis.
• Describe how pangenome approaches move beyond single reference genomes.
• Apply methods to compare and explore genomic data at scale.
• Evaluate analytical strategies in relation to biological aims and computational limits.
• Design a high-level scalable genomics plan for their own research.

The course will start on Sunday, 11th October 2026, 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, guided practical exercises, and discussion sessions designed to build conceptual understanding and analytical confidence. Learning materials will cover:

• Principles of scalable genomics and the shift beyond single reference genomes
• k-mers as a foundation for genome analysis and comparison
• Genome profiling and reference-free quality assessment
• Limitations of linear references and introduction to pangenome concepts
• Representing genomic diversity using graph-based and comparative frameworks
• Strategies for comparing multiple genomes efficiently at scale
• Considerations for computational performance, indexing, and workflow design

Friday: A group-based project session will provide an opportunity to apply the concepts covered during the week. Participants will design scalable analysis strategies in response to defined biological questions, using either their own data or example datasets. The focus will be on analytical reasoning, method selection, and workflow planning.

Training Team and Organisers

Kamil Jaron
Group Leader, Wellcome Sanger Institute

Katharine Jenike
Postdoctoral Researcher, University of Cambridge

Richard Durbin
Professor, University of Cambridge

Wellcome Connecting Science Team 

Vaishnavi Gangadhar
Informatics Technical Office

Martin Aslett
Informatics Manager

Lucy Criddle
Event Organiser

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:  22 June 2026 

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 

We can provide an option without accommodation for this event at a cost of £427.00.

If you do not require accommodation, please apply as normal and inform the event organiser if you are selected.

*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 (now extended to 1st April 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.

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