Comparison of the Nanopore and PacBio sequencing technologies for DNA 5-methylcytosine detection

DNA methylation provides a pivotal layer of epigenetic regulation in eukaryotes that has significant involvement for numerous biological processes in health and disease. Recent long-read sequencing technology including Oxford Nanopore sequencing and PacBio HiFi sequencing greatly expands the capacity of long-range, single-molecule, and direct DNA modification detection from reads without extra laboratory techniques. A growing number of analytical pipelines including base-calling and 5mC methylation detection have been developed, but there is still a lack of comprehensive evaluations of the two sequencing technologies. Here, we assess the performance of different methylation-calling pipelines based on Nanopore and HiFi sequencing datasets to provide a systematic evaluation to guide researchers on how to select the long-read sequencing technologies in performing human epigenome-wide studies.