Next Generation Sequencing Bioinformatics (Montevideo, Uruguay)

February 18th - 23rd 2018

Montevideo, Uruguay

Summary

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
course 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.

This course is open to applicants from Latin America and the Caribbean.
The course is free to attend for non-commercial applicants. Limited
bursaries to cover travel, accommodation and sustenance costs are also
available. The course will be taught in English with language support
from regional instructors.

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 commad 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 Overseas Courses in Latin America

Clinical microbiologists and public health scientists may be interested
in our Genomics and Epidemiological Surveillance of Bacterial
Pathogens
course, scheduled for July 2018 in Costa Rica,

Email us to be
notified when this course opens for applications
.
Details on previous course content can be found by clicking here.

Research scientists working on bacterial and eukaryotic pathogens may
wish to consider our Working with Pathogen
Genomes
course, scheduled for November 2018 in Uruguay.
Email us to be notified when this course opens for applications
.

Details on previous course content can be found by clicking here.

Programme

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
  • Introduction to the 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
  • 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 should be able to:

  • Use the unix command-line
  • Understand how to do QC assessment of high throughput sequencing data
  • Understand the algorithmic concepts behind short read alignment and variant calling, and practical experience using the software
  • Analyse RNA-Seq and CHiP-seq data for measuring abundance
  • Understand the organisation and sequencing data types available in public sequencing repositories
  • Evaluate the strengths, weaknesses and limitations of different bioinformatic approaches
  • Write basic shell scripts for automating bioinformatics tasks

Instructors and speakers

Course lead instructors
Thomas
Keane
EMBL-European Bioinformatics Institute, UK
Jacqui
Keane
Wellcome Trust Sanger Institute, UK
Marcela Sjoberg Herrera Pontificia Universidad Católica de Chile

How to apply

Prerequisites
This course is open to applicants from Latin America and the Caribbean.
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.

The course will be taught in English with language support from regional
instructors.

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/

Cost
Overseas courses are free to attend for non-commercial
applicants. Please contact us for the commercial fee. Limited bursaries
to cover travel, accommodation and sustenance costs are also available.
Please see the “Costs/Bursaries” tab for further details.

Applications
Applications for this course can be completed 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 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: 3 November 2017

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

Cost and bursaries

Cost
Overseas courses are free to attend for non-commercial applicants. Please
contact us for the commercial fee.

Bursaries

Limited bursaries to cover travel, accommodation and sustenance costs are
available 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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