Genome bioinformatics: from short- to long-read sequencing

A guide to the technology, analysis workflows, tools, and resources for next-generation sequencing data analysis.

This course will provide insights and training into how biological knowledge can be derived from genomics experiments and explain different approaches in analysing such data. The main focus will be on introducing sequence informatics, re-sequencing, differences between short- and long-read sequencing, and variant calling during the analysis of higher-eukaryotes, with an emphasis on human genetic research. Throughout the week, more advanced topics will introduce the creation of pipelines, automation, and the scaling-up of analysis experiments.

Who is this course for?

The course is aimed at PhD students and post-doctoral researchers who are starting to use high-throughput sequencing technologies and bioinformatics methods in their research. The content is most applicable to those working with eukaryotic genomes, especially in human genomics.

Participants will need knowledge of the Unix command line and BASH to adequately complete the practical sessions. Additionally, a short pre-course session on BASH and Unix.

Please note that participants without basic knowledge of these resources will find it difficult to complete the practical sessions.

What will I learn?

Learning outcomes

After the course, you should be able to:

• State the advantages and limitations of short- and long-read sequencing technologies
• Apply appropriate QC and aligners to unassembled short- and long-reads
• Perform variant calling analysis and annotation
• Create, scale-up, and automate genomics pipelines
• Access genomic datasets from online public resources

Course content

During this course, you will learn about: 

• Quality control methods for cleaning raw sequencing data
• Alignment of reads to a reference genome
• File format conversion and processing
• Tools for variant calling (both single-nucleotide and copy-number analysis)
• Approaches for scaling up and reproducible research

Trainers

Please read our support page before starting your application. To be considered for a place on this course, you must do the following:

• Complete the online application form.
• Ensure you add relevant information to the ‘submission details’ section where you are asked to provide information on your:
  • pre-requisite skills and knowledge
  • current work and course expectations
  • data availability
• Upload one letter of support from your supervisor or a senior colleague detailing reasons why you should be selected for the course.

Please submit all documents during the application process by 23:59 GMT on  2 August 2026. Items marked * in the application are mandatory. Incomplete applications will not be processed. 

All applicants will be informed of the status of their application (successful, waiting list, unsuccessful) two weeks after the application closing date.  If you have any questions regarding the application process, please contact Omotoke Labiyi.

Fees

Registration fees 
Payment must be completed within 14 days of receiving your acceptance email. Failure to do so may result in your place being offered to someone else on the waitlist.

Your registration fee includes:

• Catering as detailed in the course programme
• Accommodation for four nights (16, 17, 18, and 19 November) at Hinxton Hall Conference Centre.
• Bespoke course handbook with links to all course materials
• Use of a computer in the EMBL-EBI training suite throughout the course
• Secure virtual machines for the practical sessions listed in the programme
• Shuttle bus on the final course day to Cambridge train station
• Certificate on completion of the course 

* If your company is an EMBL-EBI Industry Programme Member, discounts may be available. This will apply automatically on registration if applicable; alternatively, please contact your Event Organiser for more information.

Financial assistance
Financial assistance is available to a limited number of participants attending this course.

Registration fee waivers
A limited number of registration fee waivers are offered for this course.

• Application process:
  • Apply for the fee waiver alongside your course application.
  • Provide a brief explanation of why you require the waiver and how attending the course will benefit your career.
• Notification:
  • You will be informed of your waiver status at the same time as the outcome of your course application.
  • If awarded, the registration fee will be waived entirely.

Travel grants
A limited number of travel grants of up to £1,000.00 are available to potentially support your travel expenses.

• Covered expenses:
  • Airfare, train, bus, taxi, and visa costs.
• Application process:
  • Apply for the travel grant when submitting your course application.
  • You will be informed of the grant decision, including the amount awarded, along with your course application outcome.
• Reimbursement process:
  • Participants must pay upfront for their travel costs.
  • A reimbursement form will be provided upon course completion.
  • Submit the completed form with receipts to your Event Organiser within one month of travel completion.
• Grant adjustment:
  • The organisers may adjust the grant amount to accommodate more participants.

Financial assistance terms and conditions

• Selection process: Recipients of financial assistance will be selected by the scientific organisers during the course application review.
• Selection criteria:
  • Selection is based on scientific merit, your current work or study location, the need for financial support, and the career impact of attending the course.
  • Priority will be given to applicants from Low- and Middle-Income Countries (LMICs).
• Fair consideration: Applying for financial assistance will not impact the outcome of your course application.

Additional information

Posters
If selected for this course, you will be asked to submit your poster upon registration. We expect the posters to act as a talking point between you, other attendees, and the trainers on the course. They should give the reader an idea of the work you are engaged in, what you are planning to do next, and anything of interest that might be useful for sharing with the group.

Flash talks
If selected for this course, you will be asked to submit your flash talk upon registration. This should be a short presentation about your research work, providing you with an opportunity to share your research with the other attendees and provide a forum for discussion.

Event terms and conditions

• Selection process: Recipients will be selected by the scientific organisers during the course application review.
• Selection criteria:
  • Selection is based on scientific merit, your current work or study location, the need for financial support, and the career impact of attending the course.
  • Priority will be given to applicants from Low- and Middle-Income Countries (LMICs).
• Fair consideration: Applying for financial assistance will not affect your course application outcome.

Course materials
The materials for the 2025 course are available for you to browse. These provide a snapshot of the content that will be covered in the 2026 course.