[BBC] [Gtpb] CPANG18 - Computational PANgenomics - Course Announcement
GTPB Administration
bicourses at igc.gulbenkian.pt
Tue Jan 30 12:19:35 CET 2018
ANNOUNCEMENT
CPANG18
Computational PANgenomics
with Tobias Marschall and Erik Garrison
The GTPB is proud to announce that the above referenced hands-on
training course is open for applications
IMPORTANT DATES for this Course
Deadline for applications: February 23rd 2018
Course date: March 6th - March 9th 2018
Candidates with adequate profile will be accepted in the next 72 hours
after the application until we reach 20 participants.
Course Description
Reference genomes have become central to bioinformatics approaches,
and form the core of standard analyses using contemporary sequencing
data. However, the use of linear reference genomes, which provide the
sequence of one representative genome for a species, is increasingly
becoming a limitation as the number of sequenced genomes grows. In
particular, they tend to bias us away from the observation of
variation in the genomes we study.
A general solution to this problem is to use a pangenome that
incorporates both sequence and variation from many individuals as our
reference system. This pangenome is naturally modeled as a graph with
annotations, and can provide all the functionality traditionally
provided by linear reference genomes. Unlike linear reference genomes,
a pangenome readily incorporates both small and large variation,
allowing bias-free genotyping at known alleles.
In this course we will explore the use of modern bioinformatic tools
that allow researchers to use pangenomes as their reference system
when engaging in studies of organisms of all types. Such techniques
will aid any researcher working on organisms of high genetic diversity
or on organisms lacking a high-quality reference genome. This course
targets all researchers interested in learning about an exciting
paradigm shift in computational genomics.
Objectives
Participants first will learn about limitations of linear
reference-based methods and work through a brief refresher or
introduction to standard approaches for processing sequencing data,
including read alignment and variant calling. Provided these
motivating examples, we will use data from a variety of relevant
sources to develop an intuition about pangenomic methods and a
practical familiarity with applicable tools.
More information, and access to the application process here:
http://gtpb.igc.gulbenkian.pt/bicourses/2018/PANG18
Ref:
Computational pan-genomics: status, promises and challenges
The Computational Pan-Genomics Consortium Author Notes
Briefings in Bioinformatics, Volume 19, Issue 1, 1 January 2018, Pages
118135, https://doi.org/10.1093/bib/bbw089 (OPEN ACCESS)
Hoping that this course meets your interests,
Pedro Fernandes
--
Pedro L Fernandes
Bioinformatics Training Coordinator
Instituto Gulbenkian de Ciência
Apartado 14
2781-901 OEIRAS
PORTUGAL
Tel +351 21 4407912
http://gtpb.igc.gulbenkian.pt
--
The Gulbenkian Training Programme in Bioinformatics
General Office
Rua da Quinta Grande, 6
2780-156 OEIRAS
Portugal
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