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Next Generation Sequencing

12-19 April 2015

Wellcome Trust Genome Campus, Hinxton, Cambridge

Deadline for applications: 7 November 2014

Course summary

Next-generation sequencing has become the premier tool in genetic and genomic analysis. This laboratory-based course is directed at scientists who will be generating and interpreting sequence information in their research and wish to gain a better understanding of the techniques involved and their applications. This course is not meant to replace the manufacturers’ training normally supplied with new instruments, nor is it intended to be a training course for those solely interested in next-generation sequencing bioinformatics.

The course will include theoretical and practical information on all of the next-generation sequencing systems available and those on the near horizon. The laboratory element will cover a mix of technologies that will be determined nearer the time, but will be chosen from platforms like the Ion Torrent, PacBio and Illumina Miseq / HiSeq. One aim of the course is to allow participants to make informed decisions about which technology to apply to solve specific research questions they may face in the future. A variety of applications will be covered as time permits, e.g., RNA-Seq, target enrichment, bacterial sequencing, cancer genomics, human variation analysis, etc. All the basic techniques of post-sequencing analysis will be covered, QC, alignment, assembly, variant calling, etc.

Please note: For the data analysis components of the course, applicants will require a working knowledge of the Linux operating system. This can be obtained by various methods and will be enforced.

Programme


Library Prep

• Making libraries from samples
• Both theory and practical sessions

Sequencing
• Overview: Motivation and fundamental concepts
• Detailed description of prominent sequencing technologies: current and future (3rd generation) platforms
• Hands-on laboratory work: preparing chips for sequencing and performing sequencing runs on various platforms

Data analysis
• Data QC: How to determine if a run has performed well
• Alignment to a reference, de-novo assembly, SNP and structural variant-calling of next generation DNA and RNA data
• IT and the data storage problem

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 (cancer, human diseases, pathogens, etc).

Course instructors

Tony Cox (Head of Sequencing Informatics, The Wellcome Trust Sanger Institute, Cambridge, UK)
Michael Quail (Wellcome Trust Sanger Institute, Hinxton, UK)

2014 guest speakers (2015 speakers TBA shortly)

Jeffrey Barrett (Wellcome Trust Sanger Institute, UK)
Julian Parkhill (Wellcome Trust Sanger Institute, UK)
Jenny Ekholm (Pacific Biosciences)
Elizabeth Murchison (Wellcome Trust Sanger Institute, UK)
Sarah Teichmann (European Bioinformatics Institute, EMBL-EBI, UK)

Feedback from the 2014 course

“Excellent course, very competent instructors amazing facilities and great quality of the information provided.”
“It has been the best course that I have ever attended and we were looked after so well in every aspect. Great attention to detail was paid and the organisation was excellent.”
“I feel much better equipped to be able to go back to my project and apply the skills I have learned to design and implement the NGS aspects. The small size of the group meant we received an excellent level of personal instruction and the varied backgrounds of fellow attendees was stimulating and has allowed for future collaborations.”

How to apply

Target audience and prerequisites
Applicants should be postdoctoral scientists, senior PhD students or junior faculty members actively engaged in or soon to commence research involving next generation sequencing instrumentation.

Linux experience
This course includes a substantial element of sequence data QC and analysis performed on Linux-based computers. To benefit fully from the course it is essential that successful applicants are comfortable working in a Linux-based environment prior to the course. In particular, applicants will be expected to use the command line terminal interface.

Applicants will need to be familiar with, and able to perform, the following:
creating, copying, moving and deleting text files and directories, modifying file and directory permissions, navigating directory structures, examining the contents of text files, executing programs from the command line using pipes and output redirection, compressing and decompressing files (using zip or gzip)

Cost
The course tuition fees are subsidised by the Wellcome Trust for scientists based in non-commercial institutions anywhere in the world. This is a residential course and there is a registration fee of £1000 towards board and lodging for non-commercial applicants. The fee for commercial applicants is £4200.

Bursaries
Limited bursaries are available for non-commercial applicants (up to 50 per cent of fee) and are subject to open competition. If you would like to apply for a bursary, please complete the bursary section of the online application form (see below for application process).

Applications
Application forms for this course can now be completed online. If you have any problems with the online application process, please email us.

Please note: Applications must be supported by a recommendation from a scientific sponsor. This can be your supervisor 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

Deadlines
Application deadline: 7 November 2014

Wellcome Trust, Gibbs Building, 215 Euston Road, London NW1 2BE, UK T:+44 (0)20 7611 8888