Next Generation Sequencing Bioinformatics

Next generation sequencing has become an essential tool in genetic and genomic analysis. It is increasingly important for experimental scientists to gain the bioinformatics skills required to assess and analyse the large volumes of sequencing data produced by next generation sequencers.

This next generation sequencing bioinformatics course aims to equip participants with the essential informatics skills and knowledge required to begin analysing next generation sequencing data and carry out some of the most common types of analysis.

The programme will cover the algorithmic theory and principles of bioinformatics, with a strong focus on practical computational sessions using sequence analysis techniques and tools applicable to any species or genome size. Accompanying the lecture and practical sessions will be a series of seminars by invited speakers, who will highlight their ground-breaking work in applications of next generation sequencing.

Please note: The practical sessions will be taught exclusively through Unix/Linux. Therefore, participants are required to have some previous exposure of using the Linux operating system. This will be essential for participants to fully benefit from the course.

There are numerous online introductory tutorials to the UNIX/Linux operating system and command line, including:

http://www.ee.surrey.ac.uk/Teaching/Unix
http://swcarpentry.github.io/shell-novice/

The course aims to provide a hands-on introduction to bioinformatics for next generation sequencing, and should not be considered a complete education in the theoretical and mathematical foundations of the topics.

Related courses
This course is aimed at applicants solely interested in analysis of NGS data. Applicants interested in laboratory-based training in NGS technologies and methodologies should consider our Next Generation Sequencing lab course. Email us, to be kept updated on the 2019 NGS lab course.

Researchers working on pathogen genomes may wish to consider our Working with Pathogen Genomes course, currently scheduled for March 2019. Email us to be kept updated on this course.

The hands-on programme will cover several aspects of next generation sequencing data analysis, including lectures, discussions and practical computational sessions covering the following:

• Introduction to NGS technologies and tour of Sanger Institute facilities
• Introduction to the unix command line
• Advanced unix
• NGS data formats and tools
• Sequence alignment+QC
• SNP/indel theory and practical
• Structural variation theory and practical
• RNA-seq analysis
• ChiP-seq analysis
• Sequencing data visualisation with the Integrated Genomics Viewer
• Accessing public sequencing repositories
• Participant projects and presentations (final day)

Learning Outcomes
On completion of the course, participants can expect to have acquired:

• A working knowledge of the unix command-line and advanced unix commands for automating bioinformatics tasks
• Knowledge of how to do QC assessment of high throughput sequencing data
• Understanding of the algorithmic concepts behind short read alignment and variant calling, and practical experience using the software
• Experience analysing RNA-Seq and CHiP-seq data for measuring abundance
• Knowledge of the organisation and sequencing data types available in public sequencing repositories

Course lead instructors

Guest speakers

• Frank Chan
• Claire Jenkins
• Sofia Chen
• Ximena Ibarra-Soria

Prerequisites
Applicants should be postdoctoral scientists, senior PhD students, junior faculty members or clinicians/healthcare professionals actively engaged in or soon to commence research involving next generation sequencing data analysis.

Unix/Linux experience: The practical sessions will be taught exclusively through Unix/Linux. Therefore, participants are required to have some previous exposure of using the Linux operating system. This will be essential for participants to fully benefit from the course.

There are numerous online introductory tutorials to the UNIX/Linux operating system and commad line, including:

http://www.ee.surrey.ac.uk/Teaching/Unix
http://swcarpentry.github.io/shell-novice/

How to Apply
Please complete the online application form. Places are limited and will be awarded on merit. If you have any problems with the online application process, please contact us.

Please note: Applications must be supported by a recommendation from a scientific or clinical sponsor (e.g. supervisor, line manager or head of department). A request for a supporting statement will be sent to your nominated sponsor automatically during the application process. Applicants must ensure that their sponsor provides this supporting statement by the application deadline. Applications without a supporting statement cannot be considered.

Travel visas
Successful applicants will be provided with a support letter for their visa application, if required.

Please visit the following websites for further information on visiting the UK:

• UK Border Agency website
• Information for general visitors and business visitors

*The course fee is subsidised by Wellcome Genome Campus Advanced Courses and Scientific Conferences and applies to non-commercial applicants. Please contact us for the commercial fee.

Bursaries

Limited bursaries are available (up to 50% reduction on the course fee) and are awarded on merit. If you would like to apply for a bursary, please complete the bursary section of the online application form.

Where there are many bursary applications, the selection committee may issue smaller amounts.

Bursaries can be applied for as part of the course application form. Applicants will be notified of a bursary award along with their place on the course, usually within one month of the application deadline. The decision of the selection committee is final.

Please note that both the applicant and sponsor are required to provide a justification for the bursary as part of the application.

Extra accommodation

If you wish to book onsite accommodation either side of the course dates, please contact the Conference Centre directly.

Additional funding opportunities
Visit our support page for additional financial support currently available.

Feedback from the 2017 course:

“Great course. Thanks very much”
“Thank you for a fantastic week!”
“I would like to thank the organizing committe and the instructors for the efforts they have done in the course.”
“Fantastic course!”
“I would like to thanks all the instructors, assistants, speakers and courses staff for organizing & offering this great course(specially Jacqui, Thomas and Angela), I really like it and learned a lot, it will help me now my project and further my career! I hope more and more people/students can benefit from the course!”
“Thank you very much for giving me the opportunity to attend this course”
“Thank you so much for considering me for the course and offering me a bursary to attend. My research work will be improved.”