Course: bioinformatic tools for metagenetic and population genomic data analysis (Sweden)

An introduction to bioinformatic tools for metagenetic and population
genomic data analysis
4-8 November 2013

This course aims at detailed understanding and hands-on experience of using
state of the art bioinformatics pipelines for one’s own biological research
questions. An important aspect of the course is to show how genomic data can
be applied to address and answer research questions in the fields of
genetics, ecology, population biology, biodiversity monitoring and
conservation. The students will be trained in the latest bioinformatic
methods to analyze high throughput sequencing data, which is present in many
research projects. The course will cover basic computing tools required to
run command line applications, processing high throughput sequencing data of
the CO1 gene from environmental samples to reveal biodiversity and analysis
of sequencing data from whole genome scans for population genomic studies.

The first part of the course introduces general computing tools for
beginners such as the UNIX command line environment, bash commands, data
formatting using regular expressions and basic scripting in the unix shell
with a series of examples and exercises.
The course introduces bioinformatics software for analysis of sequence data
from metagenetics (The high-throughput sequencing of a molecular marker from
an ecosystem or a community of organisms, used for large-scale analyses of
biodiversity), through a series of live demonstrations (AmpliconNoise,
TaxAssign, QIIME). The course also introduces basic and advanced concepts of
population genomics data analysis such as genome/transcriptome assembly,
annotation (BLAST), alignment/mapping, differential Gene expression,
functional enrichment tests, SNP genotyping, PCA, outlier tests.
The course corresponds to 1 week of full time studies and and is composed of
lectures, demonstrations and computer labs.

The course is limited to 12 graduate students or postdocs. There is no
course fee, but students will have to fund their own travel and lodging in
Gothenburg. All course sections take place on the Medicinareberget Campus,
Gothenburg, Sweden.

For registration, please contact Sarah Bourlat (sarah.bourlat@gu.se) or
Pierre De Wit (pierre.de_wit@gu.se)