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 genome graphs, pangenomics, the creation of pipelines, automation, and the scaling-up of analysis experiments.

Practical sessions will be run on datasets prepared by the trainers, not on personal research data. Participants will learn how to process these training datasets and to apply appropriate statistical methods in their analyses. They will also learn the basics to create their own pipelines and use pipelines openly available. 

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 for those working with eukaryotic genomes, especially in the area of human genomics.

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

Please note that participants without basic knowledge of these resources will have difficulty in completing the practical sessions.

What will I learn?

Learning outcomes

After the course participants will 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 application support page before starting your application. In order 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 BST on 3 August  2025. Items marked * in the application are mandatory. Incomplete registrations will not be processed. 

All applicants will be informed of the status of their application (successful, waiting list, unsuccessful) no later than Tuesday 26 August 2025, please note this means payments are required in the August period. If you have any questions regarding the application process please contact Anca Belu.

The registration fee includes:

• Catering as detailed on the course programme
• Accommodation for four nights (17, 18, 19, and 20 November) at Hinxton Hall Conference Centre
• Bespoke course handbook with links to the course materials
• Use of a computer in the EMBL-EBI training suite throughout the course
• Shuttle bus on the final course day to Cambridge train station 

Accommodation

Hotel rooms will be provided onsite at Hinxton Hall Conference Centre. Please contact them directly if you wish to arrange to stay additional nights around the course dates.

Catering

The course includes catering as detailed on the programme tab. Successful applicants will be asked for any dietary requirements and allergies upon registration. 

Posters

All participants are expected to present a poster that will be displayed during the course outside the training room. Successful applicants will be asked to submit their poster upon registration. We will print these for you and have them available when you arrive on site.

All posters should:

•          be A2 in size – 420mm x 594 mm
•          be in a portrait orientation
•          include your photograph and contact information

We expect the posters to act as a talking point between you, other participants and the trainers on the course. The posters will be displayed throughout the week so people can view them during breaks and lunch. 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 gathered participants.

Flash talks

All participants will be asked to give a short presentation about their research work as part of the course. These provide an opportunity to share their research with the other participants and provide a forum for discussion. Successful applicants will be required to submit their talks upon registration. 

Financial assistance

Limited financial assistance is provided by the EMBL-EBI Training in the form of registration fee waivers and travel grants. 

Your place in the course is only confirmed by paying the registration fee, which is mandatory even when receiving a fee waiver.

Registration fee waiver

The fee waiver will cover the registration fee that you have paid to attend the course.

Travel grant

The travel grant will cover the cost of travel to an on-site event (airfare, train, bus, taxi, and visa) and is capped at £1,000.00.

The organisers may reduce the grant cap to accommodate more participants. Recipients will be notified of their travel cap amount when they are informed of the outcome of their application. A reimbursement claim form with supporting receipts must be provided with your signature for all costs incurred within one month of completion of travel. 

Application

You may apply for financial assistance when submitting your application. In your application you will be asked to provide justification for the financial assistance and how your attendance will make a difference to your career. For on-site courses, please specify whether you would like to be considered for registration fee waiver, travel grant or both. Application for financial support will not affect the outcome of your course application.

Selection

The scientific organisers will select the recipients of financial assistance during the course application selection process. Results will be communicated  along with the course application outcome. Selection results do not impact your acceptance to the course. Selection for registration fee waivers and travel grants is based on scientific merit, your current work or study location, the reasons for needing financial support, and the impact this event will have on your career with priority given to applicants from low and middle income countries.

Reimbursement

Costs will be reimbursed after the course only once a reimbursement claim form and receipts (from travel costs) have been received.