{"doi":"10.1101/2021.05.05.442849","title":"DNA methylation calling tools for Oxford Nanopore sequencing: a survey and human epigenome-wide evaluation","abstract":"Abstract Background Nanopore long-read sequencing technology greatly expands the capacity of long-range single-molecule DNA-modification detection. A growing number of analytical tools have been actively developed to detect DNA methylation from Nanopore sequencing reads. Here, we examine the performance of different methylation calling tools to provide a systematic evaluation to guide practitioners for human epigenome-wide research. Results We compare five analytic frameworks for detecting DNA modification from Nanopore long-read sequencing data. We evaluate the association between genomic context, CpG methylation-detection accuracy, CpG sites coverage, and running time using Nanopore sequencing data from natural human DNA. Furthermore, we provide an online DNA methylation database ( https://nanome.jax.org ) with which to display genomic regions that exhibit differences in DNA-modification detection power among different methylation calling algorithms for nanopore sequencing data. Conclusions Our study is the first benchmark of computational methods for mammalian whole genome DNA-modification detection in Nanopore sequencing. We provide a broad foundation for cross-platform standardization, and an evaluation of analytical tools designed for genome-scale modified-base detection using Nanopore sequencing.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2021,"id":213381,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":23,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9542,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":342938,"name":"Wojciech Rosikiewicz","orcid":"0000-0001-7031-3430","position":1,"is_corresponding":false},{"id":264364,"name":"Ziwei Pan","orcid":"0000-0003-0533-1995","position":2,"is_corresponding":false},{"id":270048,"name":"Nathaniel Jillette","orcid":"0000-0003-3328-4401","position":3,"is_corresponding":false},{"id":656536,"name":"Ping Wang","orcid":"0000-0002-2710-7188","position":4,"is_corresponding":false},{"id":805320,"name":"Aziz Taghbalout","orcid":"0000-0002-6767-0258","position":5,"is_corresponding":false},{"id":227778,"name":"Jonathan Foox","orcid":"0000-0002-5705-3985","position":6,"is_corresponding":false},{"id":36370,"name":"Christopher E. Mason","orcid":"0000-0002-1850-1642","position":7,"is_corresponding":false},{"id":318325,"name":"Martin Carroll","orcid":"0000-0002-5622-3735","position":8,"is_corresponding":false},{"id":255239,"name":"Albert W. Cheng","orcid":"0000-0003-2653-5743","position":9,"is_corresponding":false},{"id":239997,"name":"Sheng Li","orcid":"0000-0002-9543-6274","position":10,"is_corresponding":false},{"id":232359,"name":"Yang Liu","orcid":"0000-0003-4433-1066","position":0,"is_corresponding":true}],"reference_count":79,"raw_metadata":null,"created_at":"2026-07-18T23:52:36.886828Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}