Whole human genome methylation analysis of the HEL cell line using nanopore sequencing

In this work, we describe the whole genome sequencing and 5’-methylcytosine (5’-mC) calling of the human erythroleukemia (HEL) cell line. Genomic DNA libraries were prepared using a rapid library preparation protocol and sequenced in the MinION device (Oxford Nanopore Technologies). Basecalling of FAST5 reads, read alignment (with ngmlr and minimap2) and methylation calling were performed using the nanopype pipeline (Giesselmann et al, 2019). We show that 10X coverage depth nanopore sequencing produces 5'-mC methylation frequencies consistent with those obtained by methylation microarray and digital restriction enzyme analysis of methylation.