Genomics and epigenetics studies across vertebrate species

SNIC 2017/1-583


SNAC Medium

Principal Investigator:

Carl-Johan Rubin


Uppsala universitet

Start Date:


End Date:


Primary Classification:

10609: Genetics (medical to be 30107 and agricultural to be 40402)

Secondary Classification:

10203: Bioinformatics (Computational Biology) (applications to be 10610)

Tertiary Classification:

10610: Bioinformatics and Systems Biology (methods development to be 10203)



In this project we will analyze primarily massively parallel single molecule sequencing data generated by various sequencing platforms, i.e. Illumina, Oxford Nanopore, PacBio and ION Proton. Previously, on milou. we had several distinct projects for the analysis of these types of data but as was suggested I hereby aim to cluster them all under a larger top project. The aims are to: (1) Learn more about the genetics of complex traits (2) Develop optimized protocols for sequencing very long reads (+100kb) using Oxford Nanopore sequencing and to utilize this data to assemble whole genomes of primarily vertebrates (Atantic Halibut, chicken and others) but also microorganisms. (3) Analyze sequencing data generated with the aim of understanding more about epigenetics, primarily 5-mC DNA methylation (5-methyl cysteine modifications of DNA), but also higher order chromatin epigenetics using methods such as HiC-libraries . For 5mC modifications we have been and will continue to generate both bisulphite sequencing data using Illumina but will also exploit the innate potential of the long-read platform Oxford nanopore sequencing to directly distinguish between methylated and non-methylated Cysteins using the raw signal from the sequencer.