This course will provide an introduction to the technology, analysis workflows, tools and resources for next generation sequencing data analysis. The content will provide insights into how biological knowledge can be derived from genomics experiments and explain different approaches to analysing such data. The main focus of the course will look at the assembly, re-sequencing, and variant calling undertaken during the analysis of higher-eukaryotes, with a particular emphasis on human genetic research.

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.

Who is this course for?

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:

• Basic introduction to the Unix environment:
  • www.ee.surrey.ac.uk/Teaching/Unix
• Introduction and exercises for Linux:
  • https://training.linuxfoundation.org/free-linux-training
• Basic R concept tutorials:
  • www.r-tutor.com/r-introduction

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:

• 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

Course content

During this course you will learn about:

• NGS 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
  • Ensembl
  • European Variation Archive
  • European Nucleotide Archive

Trainers

Please read our page on application advice before starting your application. In order to be considered for a place on this course, you must do the following:

1. Complete the online application form
2. Submit a Microsoft Word (.docx) document containing three short paragraphs with a biography, work history and description of your current research interests; each paragraph should be no more than 100 words
3. Provide a letter of support from a supervisor or a senior co-worker explaining why you should be selected for this course

Please submit all documents to Rebecca Nicholl (rnicholl@ebi.ac.uk) by 12:00 GMT on Friday 28 June, 2019.

Incomplete applications will not be considered.

Accommodation will be provided at the Holiday Inn, Impington Monday-Wednesday inclusive.  The course includes evening meals at the Hinxton Hall Restaurant on campus or the Red Lion Pub in nearby Hinxton village, and breaks and lunches outside the EMBL-EBI training rooms.