Nanopore DNA-sequencing of medaka brain samples from the MIKK panel. Indigene_nanopore_DNA_1

We used nanopore long read data to investigate further the genomic and epigenomic landscapes of a subset of the MIKK panel. Nanopore sequencing allowed us to identify a much greater variety of high quality structural variants compared with Illumina sequencing. We also present results and methods using a pan-genome graph representation of 12 individual medaka lines from the MIKK panel. By creating a graph based reference genome for the MIKK panel we are able to find novel differences between the MIKK panel lines compared to standard linear reference genomes and represent additional MIKK panel specific genomic content that would be missing from linear reference alignment approaches. We were also able to identify and quantify the presence of repeat elements such as the Teratorn fusion transposon, in each of the lines. Finally, we investigated line specific CpG methylation and performed differential DNA methylation analysis across the 12 lines analysis different lines.