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An introduction to bioinformatic tools for metagenetic and population
genomic data analysis 3-7 November 2014

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 (1.5 ECTS points)and 
is composed of lectures, demonstrations and computer labs. The course is limited to 18 graduate students or postdocs. There is no course fee, but students will have to fund their own travel.
All course sections take place at Tjärnö Marine Station, Sweden. Registration for this course is closed.


Sarah Bourlat (sarah.bourlat@gu.se) Pierre De Wit (pierre.de_wit@gu.se)


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