Analysis of High Throughput Sequencing Data


 Tuesday 23 Friday 26 October 2018


European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom

Application opens: 

Monday 23 April 2018

Application deadline: 

Friday 20 July 2018


Open application with selection


Lucie Smith

Registration fee: 

£490 - including food and accommodation

Registration closed


This course will familiarise participants with methodologies for bioinformatics analysis of next generation sequencing (NGS) data. The content will provide insights into how biological knowledge can be derived from genomics experiments and explain different approaches to analysing such data. Practical sessions will allow participants to process training datasets and apply appropriate statistical methods in their analyses.

There will be no opportunity to work with your own data during the course.


This course is aimed at PhD students and post-doctoral researchers who are using high-throughput sequencing technologies and bioinformatics methods in their research. The content is most applicable for those working with eukaryotic genomes, human genetics and in rare disease research.

Participants will require a basic knowledge of the Unix command line, the Ubuntu 16 operating system and the R statistical packages. We recommend these free tutorials:

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

Syllabus, tools and resources

During this course you will learn about:

  • High-throughput sequencing technologies
  • 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
  • Data resources for genomics data


After this course you should be able to:

  • Know the advantages and limitations of high-throughput assays
  • Assess the quality of genomic datasets
  • Compare and apply appropriate short read aligners
  • Perform variant calling analysis and variant annotation
  • Locate relevant information from online data resource

Additional information

All participants are encouraged to bring a poster that will be displayed during the course outside the training room. Posters should include information on your current research interests and how the course relates to this work. All posters should:

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

Catering is provided throughout the duration of the course. All participants will be accommodated at the Wellcome Genome Campus Conference Centre for three nights.


Time Topic Trainer
Day 1 - Tuesday 23 October 2018
12:00-13:00 Arrival, registration and lunch  
13:00-14:00 Welcome and introductions Tom Hancocks
14:00-14:30 Introduction to EMBL-EBI data resources Tom Hancocks
14:30-15:30 Introduction to Ensembl Ben Moore
15:30-16:00 Break  
16:00-17:30 European Variation Archive Baron Koylass & Andres Felipe Silva Valencia
18:00 End of day  
18:30 Check in to accommodation Conference Centre Reception
19:00 Evening meal Hinxton Hall Restaurant
Day 2 - Wednesday 24 October 2018
08:45 Arrival  
09:00-10:00 NGS technologies and library preparation Tom Hancocks
10:00-10:30 Break  
10:30-12:30 NGS data types and quality control Chiara Batini
12:30-13:30 Lunch and posters  
13:30-15:00 Read mapping; SAM/BAM format Chiara Batini
15:00-15:30 Break  
15:30-17:30 BAM refinement Chiara Batini
17:30-18:30 Group activities  
18:30 End of day  
19:00 Evening meal Hinxton Hall Restaurant
Day 3 - Thursday 25 October 2018
09:00-10:30 BAM refinement and visualisation Chiara Batini
10:30-11:00 Break  
11:00-12:30 BAM refinement and visualisation Chiara Batini
12:30-13:30 Lunch and posters  
13:30-15:30 Variant calling of SNPs Chiara Batini
15:30-16:00 Break  
16:00-17:30 Filtering variants Chiara Batini
17:30-18:30 Group activities  
18:30 End of day  
19:00 Evening meal Hinxton Hall Restaurant
Day 4 - Friday 26 October 2018
08:30 Checkout of accommodation Conference Centre Reception
08:45 Arrival  
09:00-11:00 Annotation of variants Peter Causey-Freeman
11:00-11:30 Break  
11:30-13:00 Ensembl VEP Ben Moore
13:00-13:15 Wrap-up and feedback Tom Hancocks
13:15-13:45 Lunch  
14:00 Coach to Cambridge Station