Laboratory

Next Generation Sequencing

March 11th - 17th 2016

Wellcome Genome Campus, Hinxton, UK

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
including, PacBio, Illumina Miseq/HiSeq and Oxford Nanopore MinION. 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.

Feedback from the 2015 course
“The quality and standard of this course was excellent in every
aspect.”
“I would like to say that strongly recommend this course based on the
quality, structure and working conditions offered; as well as the
knowledge, availability and good mood coordinators and instructors.”

“Generally, the course was great. -Lecture discussions complemented the
lab very well. -Lecturers/Instructors were very competent and
accommodating.”

Programme

The programme will include lecture and practical
laboratory/computer-based sessions covering the following topics:

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.

Instructors and speakers

Course instructors
Tony Cox Wellcome Trust Sanger Institute, Hinxton, UK

Michael Quail Wellcome Trust Sanger Institute, Hinxton,
UK

Guest speakers
Julian Parkhill Wellcome Trust Sanger Institute, UK

Elizabeth Murchison Wellcome Trust Sanger Institute, UK

How to apply

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 is subsidised by the Wellcome Genome Campus Advanced Courses
and Scientific Conferences Programme. This is a residential
course and
there is a fee of £1020 towards board and lodging for non-commercial
applicants. Please contact us for the commercial fee.

Applications
Applications for this course can now be completed online. 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 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.

Deadlines
Closed

Bursaries

Bursaries
Advanced Courses are subsidised for non-commercial applicants from anywhere in the world. Limited bursaries are
available (up to 50% of 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.

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

Bursary terms and conditions

UK Courses (held at the Wellcome Genome Campus, Hinxton,
Cambridge)
A
limited number of bursaries are available for each course. These are
awarded by the selection committee according to merit. The bursary
covers a maximum of 50% of the course fee, though in exceptional
circumstances an application for the total course fee may be considered.
Where there are many bursary applications, the selection committee may
issue smaller amounts. We cannot assist with travel costs to attend UK
courses.

Overseas Courses (held outside of the UK)
A
limited number of bursaries are available for each course. These are
awarded on merit to cover travel, accommodation and sustenance. The
maximum award for travel (economy class) will be £750.

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.

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