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 new 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, along with 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: Participants are required to have
experience of using the Linux operating system. This will be essential
for participants to fully benefit from the course. 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.

The hands-on programme will cover several aspects of next-generation
sequencing data analysis, including:

• Introduction to NGS technologies and tour of Sanger Institute facilities
• Introduction to unix command line
• Introduction to scripting for bioinformatics
• NGS data formats and tools
• Sequence alignment+QC
• SNP/indel theory and practical
• Structural variation theory and practical
• Sequence assembly
• RNA-seq analysis
• ChiP-seq analysis
• Accessing public repositories
• Participant projects and presentations (final day)

Course instructors
Thomas Keane Wellcome Sanger Institute, UK
Jacqui Keane Wellcome Sanger Institute, UK
Mike Quail Wellcome Sanger Institute, UK
Martin Hunt Wellcome Sanger Institute, UK
Erik Garrison Wellcome Sanger Institute, UK
Angela Goncalves Wellcome Sanger Institute, UK
Thomas Otto Wellcome Sanger Institute, UK
Adam Reid Wellcome Sanger Institute, UK
Petr Danacek Wellcome Sanger Institute, UK
Daniela Robles Espinoza Wellcome Sanger Institute, UKv
Mareike Herzog Wellcome Sanger Institute, UK
Anthony Doran Wellcome Sanger Institute, UK
Dirk Dolle Wellcome Sanger Institute, UK
Mamun Rashid Wellcome Sanger Institute, UK
Andrew Page Wellcome Sanger Institute, UK
Nishadi De Silva Wellcome Sanger Institute, UK
Daniel Gaffney Wellcome Sanger Institute, UK

Guest speakers
Nick Loman University of Birmingham
Alison Mather Wellcome Sanger Institute, UK
Benedict Paten University of California Santa Cruz,
USA

Laura Reinholdt The Jackson Laboratory, USA

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 data analysis.

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, and 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 £650 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
Deadline for Applications: Closed

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.