Methylation analysis

PacBio HiFi sequencing data can also be used to detect some types of epigenetic modifications. We used the ccsmeth v.0.3.2 (^{Ni, et al. 2022}) package to detect 5-methylcytosine base modifications in a CpG context (5mCpGs). Specifically, putative per-base modification information was first detected using the PacBio software CCS v.6.4.0 (flag '--hifi-kinetics'; https://github.com/PacificBiosciences/ccs) followed by alignment to the target genome using pbmm2 v1.7.0 (https://github.com/PacificBiosciences/pbmm2). ccsmeth then applies a deep-learning-based model (here, model_ccsmeth_5mCpG_aggregate_attbigru_b11.v2.ckpt) to infer methylation state across the target genome. Analyses with ccsmeth were done using a NVIDIA RTX 3090 graphical processing unit (GPU).