Course at EMBL-EBI
Genome bioinformatics: from short- to long-read sequencing
2024
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 GitHub, in order to adequately complete the practical sessions. Additionally, a short pre-course session on BASH and Github 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
Chiara Batini
University of Leicester Jorge Batista da Rocha
EMBL-EBI Kayesha Coley
University of Leicester Victor Flores López
University of Cambridge Erik Garrison
University of Tennessee Health Science Center Jose Maria Gonzalez Perez-Silva
EMBL-EBI Pille Hallast
The Jackson Laboratory Mohab Helmy Abdelfattah Mostafa Elbishbishy
EMBL-EBI Sarah Hunt
EMBL-EBI Sean Laidlaw
Wellcome Sanger Institute Aleena Mushtaq
EMBL-EBI Raheleh Rahbari
Wellcome Sanger Institute Charles Solomon
University of Leicester Maxime Tarabichi
Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM)
Programme
Note: Please note that the programme is still subject to changes. All times in the programme are listed in GMT.
Time
Topic
Trainer
Pre-course session (virtual) – 14 November 2024
12:00 – 15:30
Introduction to BASH and GitHub
Kayesha Coley and Sean Laidlaw
Day one – Monday 18 November 2024
11:00 – 11:30
Arrival and registration
11:30 – 12:00
Welcome and introduction to EMBL-EBI
Daniel V. Thomas Lopez
12:00 – 13:00
Overview of NGS technologies
Chiara Batini and Pille Hallast
13:00 – 14:00
Lunch
14:00 – 14:30
Flashtalks from participants I
Participants
14:30 – 15:30
Quality control
Charles Solomon and Chiara Batini
15:30 – 16:00
Break
16:00 – 17:30
Read mapping
Charles Solomon and Chiara Batini
17:30 – 18:00
Flashtalks from participants II
Participants
18:00
End of day one
18:00 – 18:30
Check-in at Hinxton Hall
18:30
Dinner at Hinxton Hall
Day two – Tuesday 19 November 2024
09:00 – 09:30
Recap of day one
Participants
09:30 – 11:00
SAM/BAM file formats – BAM refinement, QC, and visualisation, part one
Chiara Batini
11:00 – 11:30
Break
11:30 – 12:30
Fundamentals of Genome Assembly
Victor Flores Lopez
12:30 – 13:30
Lunch
13:30 – 15:00
Introduction to Variant calling. SNPs and indels
Raheleh Rahbari
15:00 – 15:30
Break
15:30 – 17:30
Variant calling and filtering through short-read sequencing (SNPs and indels) – practical
Raheleh Rahbari
17:30 – 17:45
Break
17:45 – 19:30
Group one poster sessions with dinner and nibbles
19:30
End of day two
Day three – Wednesday 20 November 2024
09:00 – 09:30
Recap of day two
Participants
09:30 – 11:00
Variant calling (SVs and CNVs) – lecture
Maxime Tarabachi
11:00 – 11:30
Break
11:30 – 13:00
Variant calling (SVs and CNVs) – practical
Maxime Tarabachi
13:00 – 14:00
Lunch
14:00 – 15:15
Annotation and Variation with Ensembl
Jose Maria Gonzalez Perez-Silva and Sarah Hunt
15:15 – 15:45
Break
15:45 – 17:00
Ensembl Variant Effect Predictor
Aleena Mushtaq and Jorge Batista da Rocha
17:00 – 18:00 Group two poster session 18:00
End of day three
19:00
Dinner at The Red Lion, Hinxton
Day four – Thursday 21 November 2024
09:00 – 09:30
Recap of day three
Participants
09:30 – 10:30
Introduction to long-read sequencing technologies
Mohab Helmy
10:30 – 11:00
Break
11:00 – 13:00
Long-read sequencing: alignment, assembly, and variant calling Mohab Helmy
13:00 – 14:00
Lunch
14:00 – 16:00
Long-read sequencing: alignment, assembly, and variant calling (continued)
Mohab Helmy
16:00 – 16:30
Break
16:30 – 18:00
Long-read sequencing: Genome graphs and Pangenomics
Mohab Helmy
18:00
End of day four
18:30
Dinner at Hinxton Hall
Day five – Friday 22 November 2024
09:00 – 09:30
Recap of day four
Participants
09:30 – 11:30
Scaling things up: Genome bioinformatics on clusters & parallel computing – lecture and practical
Sean Laidlaw
11:30 – 12:00
Break
12:00 – 13:00
Building a pipeline
Victor Flores Lopez
13:00 – 14:00
Lunch
14:00 – 15:00
Building a pipeline (continued), optimising your analysis and interpreting results
Victor Flores Lopez
15:00 – 15:45
Keynote: Human Pangenome Consortium
Erik Garrison
15:45 – 16:15
Course wrap-up and feedback
Daniel V. Thomas Lopez
16:15
End of course
16:30
Shuttle 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 £500.
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.
University of Leicester
EMBL-EBI
University of Leicester
University of Cambridge
University of Tennessee Health Science Center
EMBL-EBI
The Jackson Laboratory
EMBL-EBI
EMBL-EBI
Wellcome Sanger Institute
EMBL-EBI
Wellcome Sanger Institute
University of Leicester
Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM)
Programme
Note: Please note that the programme is still subject to changes. All times in the programme are listed in GMT.
Time | Topic | Trainer |
Pre-course session (virtual) – 14 November 2024 | ||
12:00 – 15:30 | Introduction to BASH and GitHub | Kayesha Coley and Sean Laidlaw |
Day one – Monday 18 November 2024 | ||
11:00 – 11:30 | Arrival and registration | |
11:30 – 12:00 | Welcome and introduction to EMBL-EBI | Daniel V. Thomas Lopez |
12:00 – 13:00 | Overview of NGS technologies | Chiara Batini and Pille Hallast |
13:00 – 14:00 | Lunch | |
14:00 – 14:30 | Flashtalks from participants I | Participants |
14:30 – 15:30 | Quality control | Charles Solomon and Chiara Batini |
15:30 – 16:00 | Break | |
16:00 – 17:30 | Read mapping | Charles Solomon and Chiara Batini |
17:30 – 18:00 | Flashtalks from participants II | Participants |
18:00 | End of day one | |
18:00 – 18:30 | Check-in at Hinxton Hall | |
18:30 | Dinner at Hinxton Hall | |
Day two – Tuesday 19 November 2024 | ||
09:00 – 09:30 | Recap of day one | Participants |
09:30 – 11:00 | SAM/BAM file formats – BAM refinement, QC, and visualisation, part one | Chiara Batini |
11:00 – 11:30 | Break | |
11:30 – 12:30 | Fundamentals of Genome Assembly | Victor Flores Lopez |
12:30 – 13:30 | Lunch | |
13:30 – 15:00 | Introduction to Variant calling. SNPs and indels | Raheleh Rahbari |
15:00 – 15:30 | Break | |
15:30 – 17:30 | Variant calling and filtering through short-read sequencing (SNPs and indels) – practical | Raheleh Rahbari |
17:30 – 17:45 | Break | |
17:45 – 19:30 | Group one poster sessions with dinner and nibbles | |
19:30 | End of day two | |
Day three – Wednesday 20 November 2024 | ||
09:00 – 09:30 | Recap of day two | Participants |
09:30 – 11:00 | Variant calling (SVs and CNVs) – lecture | Maxime Tarabachi |
11:00 – 11:30 | Break | |
11:30 – 13:00 | Variant calling (SVs and CNVs) – practical | Maxime Tarabachi |
13:00 – 14:00 | Lunch | |
14:00 – 15:15 | Annotation and Variation with Ensembl | Jose Maria Gonzalez Perez-Silva and Sarah Hunt |
15:15 – 15:45 | Break | |
15:45 – 17:00 | Ensembl Variant Effect Predictor | Aleena Mushtaq and Jorge Batista da Rocha |
17:00 – 18:00 | Group two poster session | |
18:00 | End of day three | |
19:00 | Dinner at The Red Lion, Hinxton | |
Day four – Thursday 21 November 2024 | ||
09:00 – 09:30 | Recap of day three | Participants |
09:30 – 10:30 | Introduction to long-read sequencing technologies | Mohab Helmy |
10:30 – 11:00 | Break | |
11:00 – 13:00 | Long-read sequencing: alignment, assembly, and variant calling | Mohab Helmy |
13:00 – 14:00 | Lunch | |
14:00 – 16:00 | Long-read sequencing: alignment, assembly, and variant calling (continued) | Mohab Helmy |
16:00 – 16:30 | Break | |
16:30 – 18:00 | Long-read sequencing: Genome graphs and Pangenomics | Mohab Helmy |
18:00 | End of day four | |
18:30 | Dinner at Hinxton Hall | |
Day five – Friday 22 November 2024 | ||
09:00 – 09:30 | Recap of day four | Participants |
09:30 – 11:30 | Scaling things up: Genome bioinformatics on clusters & parallel computing – lecture and practical | Sean Laidlaw |
11:30 – 12:00 | Break | |
12:00 – 13:00 | Building a pipeline | Victor Flores Lopez |
13:00 – 14:00 | Lunch | |
14:00 – 15:00 | Building a pipeline (continued), optimising your analysis and interpreting results | Victor Flores Lopez |
15:00 – 15:45 | Keynote: Human Pangenome Consortium | Erik Garrison |
15:45 – 16:15 | Course wrap-up and feedback | Daniel V. Thomas Lopez |
16:15 | End of course | |
16:30 | Shuttle 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 £500.
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.