Virtual course
Next generation sequencing bioinformatics
A guide to the technology, analysis workflows, tools, and resources for next generation sequencing data analysis.
This virtual course will provide insights into how biological knowledge can be derived from genomics experiments and explain different approaches in analysing such data. The main focus will be on assembly, re-sequencing, and variant calling during the analysis of higher-eukaryotes, with a particular 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.
Practical sessions will enable participants to process training datasets and apply appropriate statistical methods in their analyses. There will be no opportunity to work with personal research data during the course.
Virtual course
Participants will learn via a mix of pre-recorded lectures, live presentations, and trainer Q&A sessions. Practical experience will be developed through group activities and trainer-led computational exercises. Live sessions will be delivered using Zoom with additional support and communication via Slack.
Pre-recorded material will be made available to registered participants prior to the start of the course and in the week before the course there will be a brief induction session. Computational practicals will run on EMBL-EBI's virtual training infrastructure, meaning participants will not require access to a powerful computer or install complex software on their own machines.
Participants will need to be available between the hours of 09:30-17:30 GMT each day of the course. Trainers will be available to assist, answer questions and further explain the analysis during these times.
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 genetics and rare-disease research.
Participants will require a basic knowledge of the Unix command line and the Ubuntu 18 operating system. We recommend these free tutorials:
- Basic introduction to the Unix environment:
- Introduction and exercises for Linux:
Please note: participants without basic knowledge of these resources will have difficulty in completing the practical sessions.
What will I learn?
Learning outcomes
After this course you should be able to:
- State the advantages and limitations of high-throughput assays
- Apply appropriate short read aligners to unassembled reads
- Perform variant calling analysis and annotation
- Scale-up and automate simple genomics pipelines
- Access genomic datasets from online public resources
Course content
During this course you will learn about:
- Quality control methods for cleaning raw read data
- Alignment of reads to a reference genome
- File format conversion and processing
- Tools for variant calling
- Methodologies for variant annotation
- Approaches for scaling up and reproducing data
- Data resources for genomics data
Trainers
EMBL-EBI
University of Leicester
University of Leicester
University of Leicester
University of Leicester
Wellcome Sanger Institute
Wellcome Sanger Institute
The Alan Turing Institute
EMBL-EBI
Wellcome Sanger Institute
EMBL-EBI
EMBL-EBI
Wellcome Sanger Institute
Programme
Day 1 – Monday 15 February 2021 |
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09:30-09:45 | Arrival, registration, and hangout | Tom Hancocks & Marina Pujol | |||||||
09:45-10:00 | Introduction to virtual training | Tom Hancocks | |||||||
10:00-10:45 | Welcome and introductions | Tom Hancocks & Chiara Batini | |||||||
10:45-11:00 | Break | ||||||||
11:00-12:00 | Overview of NGS technology | Chiara Batini | |||||||
12:00-13:00 | Introduction to Unix |
Chiara Batini, Charles Solomon, Kayesha Coley & Noemi Piga |
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13:00-14:00 | Break | ||||||||
14:00-14:30 | Quality control - lecture | Chiara Batini | |||||||
14:30-15:30 | Quality control - practical | Chiara Batini | |||||||
15:30-15:45 | Break | ||||||||
15:45-16:15 | Read mapping - lecture | Chiara Batini | |||||||
16:15-17:00 | Read mapping - practical | Chiara Batini | |||||||
17:00-17:30 | Flash presentations | All | |||||||
17:30 | End of day | ||||||||
Day 2 – Tuesday 16 February 2021 |
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09:30-09:45 | Arrival, registration, and hangout | Tom Hancocks & Marina Pujol | |||||||
09:45-10:00 | Recap of Day 1 | All | |||||||
10:00-10:45 | SAM/BAM file formats - lecture | Chiara Batini | |||||||
10:45-11:45 | SAM/BAM file formats - practical | Chiara Batini | |||||||
11:45-12:00 | Break | ||||||||
12:00-13:00 | Introduction to BASH, loops, and variables | Chiara Batini, Charles Solomon, Kayesha Coley & Noemi Piga | |||||||
13:00-14:00 | Break | ||||||||
14:00-15:00 | BAM refinement, QC & visualisation - lecture | Chiara Batini | |||||||
15:00-16:00 | BAM refinement, QC & visualisation - practical | Chiara Batini | |||||||
16:00-16:15 | Break | ||||||||
16:15-17:00 | BAM refinement, QC & visualisation - practical | Chiara Batini | |||||||
17:00-17:30 | Flash presentations | All | |||||||
17:30 | End of day | ||||||||
Day 3 – Wednesday 17 February 2021 |
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09:30-09:45 | Arrival, registration, and hangout | Tom Hancocks & Marina Pujol | |||||||
09:45-10:00 | Recap of Day 2 | All | |||||||
10:00-10:45 | Variant calling - lecture | Chiara Batini | |||||||
10:45-11:45 | Variant calling - practical | Chiara Batini | |||||||
11:45-12:00 | Break | ||||||||
12:00-13:00 | Introduction to GitHub | Sean Laidlaw & Raheleh Rahbari | |||||||
13:00-14:00 | Break | ||||||||
14:00-15:00 | Variant filtering - lecture | Chiara Batini | |||||||
15:00-16:00 | Variant filtering - practical | Chiara Batini | |||||||
16:00-16:15 | Break | ||||||||
16:15-17:00 | Variant filtering - practical | Chiara Batini | |||||||
17:00-17:30 | Flash presentations | All | |||||||
17:30 | End of day | ||||||||
Day 4 – Thursday 18 February 2021 |
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09:30-09:45 | Arrival, registration, and hangout | Tom Hancocks & Marina Pujol | |||||||
09:45-10:00 | Recap of Day 3 | All | |||||||
10:00-10:45 | Scaling things up - lecture | Sean Laidlaw & Raheleh Rahbari | |||||||
10:45-11:45 | Scaling things up - practical | Sean Laidlaw & Raheleh Rahbari | |||||||
11:45-12:00 | Break | ||||||||
12:00-13:00 | Scaling things up - practical | Sean Laidlaw & Raheleh Rahbari | |||||||
13:00-14:00 | Break | ||||||||
14:00-15:30 | Introduction to Docker | Sean Laidlaw & Raheleh Rahbari | |||||||
15:30-15:45 | Break | ||||||||
15:45-17:00 | The Turing Way and reproducible research aspects of data science | Malvika Sharan | |||||||
17:00-17:30 | Flash presentations | All | |||||||
17:30 | End of day | ||||||||
Day 5 – Friday 19 February 2021 |
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09:30-09:45 | Arrival, registration and hangout | Tom Hancocks & Marina Pujol | |||||||
09:45-10:00 | Recap of Day 4 | All | |||||||
10:00-11:45 | Ensembl genome browser & VEP | Emily Perry | |||||||
11:45-12:00 | Break | ||||||||
12:00-12:40 | Genomic pipelines in the Darwin Tree of Life project | Marcela Uliano-Silva | |||||||
12:40-13:00 | Manual genome annotation | Alan Tracey | |||||||
13:00-14:00 | Break | ||||||||
14:00-15:30 | European Nucleotide Archive | Sam Holt | |||||||
15:30-15:45 | Break | ||||||||
15:45-17:00 | European Variation Archive | Baron Koylass | |||||||
17:00-17:30 | Course wrap-up & feedback | Tom Hancocks & Marina Pujol | |||||||
17:30 | End of course |
Before starting your application please read our application advice page. In order to be considered for a place on this course, you must submit a complete application which includes the following sections:
- Complete the online application form providing answers as directed
- Ensure you add relevant information to the "Application submission" section where you are asked to provide three 100-word paragraphs to describe your:
- scientific biography
- work history
- current research interests
- Upload a 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 midnight on Friday 27 November 2020.
Incomplete applications will not be considered.
All applicants will be informed of the status of their application (successful, waiting list, rejected) by Friday 11 December 2020. If you have any questions regarding the application process please contact Marina Pujol (mpujol@ebi.ac.uk).
Participant 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. Further details will be provided following registration
Participant scientific poster
There will be an additional opportunity for all participants to submit a poster which will be shared with the trainers and other participants alongside a scientific biography. The poster is an opportunity to provide further information about their research and stimulate more discussions between course participants. Further details will be provided following registration.
Competency frameworks define a core set of competencies required by professionals working in a specific field.
Visit the Competency Hub to learn more about what competencies are and to view a range of competency frameworks, career profiles, and training resources to support career development in the life sciences.
This course currently has no associated competencies.