An introduction to bioinformatic tools for population genomic data analysis

Third-cycle level | 2.5 credits | Course code: NMAR302
HT 2020
Study period: 2020-11-09 - 2020-11-13
LANGUAGE OF INSTRUCTION: The course is given in English
Application period: 2020-09-08 - 2020-10-25
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Course description

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 whole genome / exome / restriction site digested (RAD) DNA 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 using a remote server. The course introduces bioinformatics software for analysis of RAD-data, and downstream population genetic analysis of genotype data. The course also introduces basic and advanced concepts of population genomics data analysis such as genome/transcriptome assembly, 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.

Requirements and Selection

Entry requirements

Admitted to third cycle education

Selection

When there are more qualified applicants than the number of places on the course, a selection must be made according to this priority order:

     1 PhD students at the Faculty of Science
     2 PhD students at another faculty of Gothenburg University
     3 PhD students accepted at Chalmers
     4 PhD students accepted at other universities

Other information

The course is limited to 18 graduate students or postdocs. There is nocourse fee, but students will have to fund their own travel.All course sections take place at Tjärnö Marine Laboratory, Sweden.

The 2020 implementation of the course will depend on the Covid-19 situation, and will not be offered if travel restrictions are in place.

Course syllabus

NMAR302

Department

Department of Marine Sciences

CONTACTPierre de Wit
0317869550
pierre.de_wit@marine.gu.se