Open-access bioinformatics pipeline to extract DNA variants for genomic studies

Aquaculture breeding programmes as well as studies on determination of genetic variants related to complex fish traits and population structures can be improved through the analyses of genomic, DNA-level variation. A laboratory and bioinformatics pipeline is crucial to generate data for such analysis, but so far it does not exist for European whitefish (Coregonus lavaretus L.). Luke has now developed the pipeline, as part of the project ARCTAQUA, to extract DNA variants along the whole genome and to produce genomic data from tissue samples collected from thousands of individuals. The method will be applied to improve breeding and fish welfare traits of European whitefish. The bioinformatics pipeline is freely available on GitHub: https://github.com/fischuu/Pipeline-GBS.

The experts behind the efforts are Oliver Bitz and Daniel Fischer.