DNA methylation calling from ONT data and CpG island prediction

Basecalled ONT reads previously used for the genome assembly were aligned back to the IMR_Hiphip.v1 assembly using minimap2. The software nanopolish [71] was used to index the raw ONT fast5-files to enable extraction of likelihoods of CpG site methylation along individual mapped reads in genome assembly coordinates. Next, the nanopolish script “calculate_methylation_frequency.py” was used to extract the methylation frequency at each adequately covered CpG cluster in the assembly. CpG islands were predicted for the IMR_Hiphip.v1 assembly using gcluster [72] employing default settings.