{"doi":"10.1101/2025.05.22.655567","title":"GPatch enables chromosome-scale, gap-free pseudoassemblies from fragmented draft genomes","abstract":"Recent advancements in sequencing technologies have yielded numerous long-read draft genomes, promising to enhance our understanding of genomic variation. However, draft genomes are typically highly fragmented, posing significant challenges for functional genomics. We introduce GPatch, a tool that constructs chromosome-scale pseudoassemblies from fragmented drafts using alignments to a reference genome. GPatch produces complete, accurate, gap-free assemblies preserving over 95% of nucleotides from draft genomes. We show that GPatch assemblies can be used as references for Hi-C data analysis, whereas draft assemblies cannot. Until complete genome assembly becomes routine, GPatch presents a necessary tool for maximizing the utility of draft genomes.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2025,"id":566804,"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":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9498,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":242216,"name":"Alan P. Boyle","orcid":"0000-0002-2081-1105","position":1,"is_corresponding":false},{"id":539752,"name":"Adam Diehl","orcid":"0000-0002-0915-4570","position":0,"is_corresponding":true}],"reference_count":33,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T02:56:40.491968Z","pmid":"40501647","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":[]}