The advent of next-generation sequencing and the era of complete genomics has brought us close to fully deciphering the human genome from ‘telomere to telomere’, as demonstrated by the growing body of scientific work, including the new human reference released by the T2T consortium. Yet, there are parts of the human genomes that are still prone to misassembly and mischaracterization, especially those that are duplicated and/or present many times in identical or nearly identical versions. Some of these sequences differ on an epigenetic level, e.g. by their methylation status. Traditionally, the differences in methylation can be detected by bisulfite sequencing, requiring additional sample processing and manipulation. Recently, long reads such as those by PacBio and Nanopore sequencing became capable of detecting these modifications. In the case of PacBio, this is achieved by detecting the altered polymerase dynamics, as the incorporation of methylated nucleotides takes longer during the sequencing process. In the case of Nanopore, methylated nucleotides alter the electrical signal when passing through the pore. The student will develop algorithms and approaches that are able to discriminate among (nearly) identical sequences based on their epigenetic profiles using long reads. Further, the student will use known published examples of such differences (e.g. for an active and inactive X chromosome) to demonstrate the performance of a proposed solution. Finally, this work will aid in the mapping and assembly of these complex regions.