Working with Pathogen Genomes

17–22 January 2016

Wellcome Genome Campus, Hinxton, UK


This five-day computational workshop aims to give molecular
microbiologists working with bacteria and eukaryotic pathogens a working
knowledge of genomic analysis, which will cover the handling and
processing of DNA sequence data produced by ‘second generation’
sequencers. The workshop will be taught by members of the Pathogen
and Parasite Genetics teams
from the Wellcome Trust Sanger Institute
and will take the form of a series of modules covering most aspects of
sequence analysis and exploitation. Each module will be introduced with a
short talk, followed by hands-on worked examples using data from
bacterial and eukaryotic pathogens.

The workshop begins with training in the use of genome analysis software
(Artemis and
), developed at the Sanger Institute for genome exploration and
comparative genomics. It then goes on to cover the mapping of Illumina
sequence data, SNP calling, genome assembly, and genome annotation. The
workshop also features a module that aims to teach the basics of using
genome/gene sequences to plot phylogenetic relationships between

Feedback from previous workshops
“This was an incredible course–very well organized and a thorough
mix of lectures and computer labs. The instructors were amazing and so
“A really excellent course with superb access to expertise. Can’t fault
it in any way.”
“Thank you! This course was invaluable to me. I left feeling re-energized
and much better informed about tools for genome exploration.”
“Great course! Probably one of the best courses I’ve attended.”


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

Introduction to Artemis/ACT
and comparative genomics

  • Using Artemis as a sequence analysis tool for prokaryote and eukaryotic genomes
  • Extensive hands on experience of the Artemis genome Comparison Tool (ACT)
  • Overview of genome sequencing strategies, assemblies and genome analysis
  • Understanding DNA sequence data formats
Analysis of genomic sequencing data
  • Mapping Illumina sequence data against a reference genome
  • Genome-wide phylogenetic analysis using SNPs
  • De novo genome assembly from short reads
  • Annotating your genome assembly using ab initio gene finders

Instructors and speakers

The workshop will be taught by members of the Pathogen and Parasite Genetics teams from the Wellcome Trust Sanger Institute.

How to apply

Applicants should have a molecular biology background and currently be
engaged in relevant research.

The workshop is subsidised by the Wellcome Genome Campus
Advanced Courses and Scientific Conferences Programme. This is a
residential workshop and there is a fee of £690 towards board and lodging
for non-commercial applicants. Please contact us for the commercial fee.

Applications for this course can 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.




Advanced Courses are subsidised for non-commercial
applicants from anywhere in the world. Additional, 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

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,
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

Overseas Courses (held outside of the UK)
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.
will be notified of a bursary award along with their place on
course, usually within one month of the application deadline. The
decision of the selection committee is

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