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:

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

Tom Hancocks
EMBL-EBI
Chiara Batini
University of Leicester
Charles Solomon
University of Leicester
Kayesha Coley
University of Leicester
Noemi Piga
University of Leicester
Sean Laidlaw
Wellcome Sanger Institute
Raheleh Rabhari
Wellcome Sanger Institute
Malvika Sharan
The Alan Turing Institute
Emily Perry
EMBL-EBI
Marcela Uliano-Silva
Wellcome Sanger Institute
Sam Holt
EMBL-EBI
Baron Koylass
EMBL-EBI
Alan Tracey
Wellcome Sanger Institute

Programme

Day 1 – Monday 15 February 2021

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

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

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

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

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

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.

 

This course has ended

15 - 19 February 2021
£200
Contact
Marina Pujol

Organisers
  • Tom Hancocks
    EMBL-EBI
  • Chiara Batini
    University of Leicester

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