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 ([email protected]) or Pierre De Wit ([email protected])
