Next Generation Sequencing

Next-generation sequencing has become the premier tool in genetic and
genomic analysis. This laboratory- and computer–based course is directed
at scientists who will be generating and interpreting sequence
information and wish to gain a better understanding of the techniques
involved and their applications.

Taught by instructors from the prestigious Wellcome Trust Sanger
Institute, the course will include theoretical and hands-on practical
training on current and emerging next-generation sequencing systems,
including,

• PacBio
• Illumina Miseq/HiSeq
• Oxford Nanopore MinION

The aim of the course is to allow participants to make informed decisions
about which technologies and methodologies to apply to solve specific
research questions they may face in the future. A variety of applications
will be covered, e.g., RNA-Seq, target enrichment, bacterial sequencing,
cancer genomics, human variation analysis, etc. All the basic techniques
of post-sequencing analysis will also be covered (QC, alignment,
assembly, variant calling, etc.).

Feedback from the 2017 course

“This very intensive course provides a comprehensive technology
spanning overview of the NGS technology: including library preparation,
introduction in several NGS platforms and detailed data analysis,
starting with LINUX introduction. I have not found any comparable other
course and I am glad to have had the opportunity to take part in it.”
“Thank you to all involved in the course. It was intense but overall a
truly fantastic experience where I learned many new skills and created
lots of new friends.”
“The Next Generation Sequencing Course 2017 helped me to stick the
laboratory side together with the bioinformatics site and helped to close
my knowledge gaps in the NGS data analysis!”
“I would like to thank everybody from the organising team of Advanced
courses to the instructors for such a wonderful,
life-time experience! I gained a lot from this course and for sure the
knowledge will help me advance to the next level of my project.”
“This was a really well conducted course and I go back with a much
greater understanding of NGS and its different aspects. Thanks to the
whole advanced courses team for making this such a great
experience!”

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
  problems

Learning Outcomes
By the end of this course participants will be able to:

• make high quality libraries for Next Generation Sequencing
• explain and evaluate a range of sequencing technologies, current and future (3rd generation) platforms
• demonstrate how to set up a sequencing run
• critically assess a sequencing run

*Linux experience
This course includes several data
analysis modules using the Linux-based
operating system. 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)

There are numerous online introductory tutorials to the UNIX/Linux
operating system and commad line, including:
http://rik.smith-unna.com/command_line_bootcamp
http://www.ee.surrey.ac.uk/Teaching/Unix
http://swcarpentry.github.io/shell-novice/

Course instructors
Tony Cox Wellcome Trust Sanger Institute, UK
Michael Quail Wellcome Trust Sanger Institute, UK
Jacqui Keane Wellcome Trust Sanger Institute, UK

Guest speakers
Daniel Gaffney Wellcome Trust Sanger Institute, UK
Elizabeth Murchison University of Cambridge, UK

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. Please also review
the Linux experience information under the Programme
tab.

Applications
Applications can be submitted online. 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.

Deadlines
Deadline for Applications: Closed

Travel visas
Please contact the
event organiser if you require a letter to support a travel visa
application. Note that letters will only be provided to confirmed attendees.

Non-European Economic Area or Swiss nationals may be required to have a
visa to enter the UK.
Early application is strongly advised, as this process can take 6-8 weeks
or longer.

Please visit the following websites for further information:
UK Border Agency website and information for general visitors and business
visitors.

Cost
The
course is subsidised by the Wellcome Genome Campus
Advanced Courses and
Scientific Conferences Programme. This is a
residential
course and the fee is £1065, including all
accommodation and meals. This subsidised fee is available to all
non-commercial applicants. Please contact us for the commercial fee.

Bursaries
Advanced Courses are subsidised for non-commercial applicants from
anywhere in the world. Additional, limited bursaries are
available (up
to a 50% reduction 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.