SBTM12: Sequence-based typing methods for micro-organisms

I'm going to be helping out with teaching the NGS-related aspects of this course which might be interesting to you if you are thinking about using whole-genome sequencing for bacterial typing. Keith Jolley will also be there, talking about his software BigsDB software and his new rMLST method for bacterial typing.

The best news is that the course will be in Lisbon in September so the presence of some sunny weather - whilst not guaranteed - is significantly more likely than in the UK! The course is also about 500m from the beach! Not that this should influence your decision to come, obviously.

Here's the skinny:

ANNOUNCEMENT

SBTM12 - SEQUENCE-BASED TYPING METHODS for MICROORGANISMS

with Keith Jolley, Nick Loman, João Carriço,
Mario Ramirez, Nuno Faria and Teresa Conceição

IMPORTANT DATES for SBTM12
Deadline for applications: September 10th 2012
Notification of acceptance dates:
EARLY: September 3rd 2012
(on special request, see Application)
NORMAL: September 12th 2012
Course date: September 25th - September 28th 2012

Course Description
Overview
Technological advances in DNA sequencing have led to the adoption of
sequence-based typing methods as the standard techniques for bacterial
identification at strain level, specially due to their portability and
reproducibility. The widespread use of remotely accessible databases
offering different typing data and the development of diverse data
analysis techniques show the impact of Bioinformatics in this field,
and the need for understanding how to operate with the databases and
algorithms. Recently, the capability of sequencing whole bacterial
genomes in a few days using Next Generation Sequencing (NGS)
methodologies, opened a new door for the development of more
sophisticated strain identification tools.

Objectives
This training course is directed for the data analysis of sequence
based typing methods, from the raw-data to the identification of a
strain type by several typing methodologies, and the use of analysis
algorithms to create groups of related strains. It will span from
Single Locus Sequence Typing methods, such as spa typing or emm
typing, to the now established MultiLocus Sequence Typing (MLST) and
Multilocus Variable Number of Tandem Repeats Analysis (MLVA)
methodologies. The course will also cover methods that apply to whole
genome sequence data, and show how NGS data can be analyzed and made
sense of, in this context.
The course will be essentially hands-on. Short presentations will be
interweaved by tutored assited exercises.
The participants are expected to gradually gain user independence by
acquiring new analytical skils in using software and online databases
for specific typing methods. Special attention will be given to
methods that can use NGS datasets.

Target Audience
This course is aimed to anyone working in molecular epidemiology, that
wants to develop or consolidate skills in the use and analysis of
sequence-based typing methods. The course will be illustrated with
examples from different bacterial species, but the concepts are
applicable to any species and to other sequence-based typing methods,
not explicitly referred to in the course.

Course Pre-requisites
Basic understanding of molecular biology, namely in microbial typing
methodologies and elementary computer interaction skills are expected.

Futher details, including application instructions available at
http://gtpb.igc.gulbenkian.pt/bicourses/SBTM12