{"doi":"10.1101/2023.04.20.537673","title":"DNA-m6A calling and integrated long-read epigenetic and genetic analysis with fibertools","abstract":"Abstract Long-read DNA sequencing has recently emerged as a powerful tool for studying both genetic and epigenetic architectures at single-molecule and single-nucleotide resolution. Long-read epigenetic studies encompass both the direct identification of native cytosine methylation as well as the identification of exogenously placed DNA N 6 -methyladenine (DNA-m6A). However, detecting DNA-m6A modifications using single-molecule sequencing, as well as co-processing single-molecule genetic and epigenetic architectures, is limited by computational demands and a lack of supporting tools. Here, we introduce fibertools , a state-of-the-art toolkit that features a semi-supervised convolutional neural network for fast and accurate identification of m6A-marked bases using PacBio single-molecule long-read sequencing, as well as the co-processing of long-read genetic and epigenetic data produced using either PacBio or Oxford Nanopore sequencing platforms. We demonstrate accurate DNA-m6A identification (>90% precision and recall) along >20 kilobase long DNA molecules with a ∼1,000-fold improvement in speed. In addition, we demonstrate that fibertools can readily integrate genetic and epigenetic data at single-molecule resolution, including the seamless conversion between molecular and reference coordinate systems, allowing for accurate genetic and epigenetic analyses of long-read data within structurally and somatically variable genomic regions.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2023,"id":390054,"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":14,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9525,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":341351,"name":"Stephanie C. Bohaczuk","orcid":"0000-0001-8802-6579","position":1,"is_corresponding":false},{"id":411304,"name":"Yizi Mao","orcid":"0000-0001-5743-6831","position":2,"is_corresponding":false},{"id":69027,"name":"Jane Ranchalis","orcid":null,"position":3,"is_corresponding":false},{"id":954252,"name":"Benjamin J. Mallory","orcid":"0000-0003-1572-6181","position":4,"is_corresponding":false},{"id":947170,"name":"Alan Min","orcid":"0000-0001-9489-0478","position":5,"is_corresponding":false},{"id":554718,"name":"Morgan O. Hamm","orcid":"0000-0003-4192-2688","position":6,"is_corresponding":false},{"id":993533,"name":"Elliott Swanson","orcid":"0000-0002-0351-6446","position":7,"is_corresponding":false},{"id":24458,"name":"Danilo Dubocanin","orcid":"0000-0003-0330-5814","position":8,"is_corresponding":false},{"id":263405,"name":"Connor Finkbeiner","orcid":"0009-0003-5466-1285","position":9,"is_corresponding":false},{"id":842329,"name":"Tony Li","orcid":"0000-0003-3546-123X","position":10,"is_corresponding":false},{"id":1161329,"name":"Dale Whittington","orcid":"0009-0004-0901-4481","position":11,"is_corresponding":false},{"id":4958,"name":"William Stafford Noble","orcid":"0000-0001-7283-4715","position":12,"is_corresponding":false},{"id":11629,"name":"Andrew B. Stergachis","orcid":"0000-0002-1299-3674","position":13,"is_corresponding":false},{"id":24561,"name":"Mitchell R. Vollger","orcid":"0000-0002-8651-1615","position":14,"is_corresponding":false},{"id":286526,"name":"Anupama Jha","orcid":"0000-0003-3029-2086","position":0,"is_corresponding":true}],"reference_count":37,"raw_metadata":null,"created_at":"2026-07-19T01:18:32.854511Z","pmid":"37131601","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":[]}