{"doi":"10.1101/2024.02.15.580432","title":"Phasing Diploid Genome Assembly Graphs with Single-Cell Strand Sequencing","abstract":"Abstract Haplotype information is crucial for biomedical and population genetics research. However, current strategies to produce de-novo haplotype-resolved assemblies often require either difficult-to-acquire parental data or an intermediate haplotype-collapsed assembly. Here, we present Graphasing, a workflow which synthesizes the global phase signal of Strand-seq with assembly graph topology to produce chromosome-scale de-novo haplotypes for diploid genomes. Graphasing readily integrates with any assembly workflow that both outputs an assembly graph and has a haplotype assembly mode. Graphasing performs comparably to trio-phasing in contiguity, phasing accuracy, and assembly quality, outperforms Hi-C in phasing accuracy, and generates human assemblies with over 18 chromosome-spanning haplotypes.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2024,"id":490304,"datarank":0.10397207708399181,"base_score":0.6931471805599453,"endowment":0.6931471805599453,"self_citation_contribution":0.10397207708399181,"citation_network_contribution":0.0,"self_endowment_contribution":0.10397207708399181,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":1,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9256,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":243998,"name":"Maryam Ghareghani","orcid":null,"position":1,"is_corresponding":false},{"id":19702,"name":"William T. Harvey","orcid":"0000-0003-0646-7528","position":2,"is_corresponding":false},{"id":19696,"name":"David Porubsky","orcid":"0000-0001-8414-8966","position":3,"is_corresponding":false},{"id":2118,"name":"Sergey Koren","orcid":"0000-0002-1472-8962","position":4,"is_corresponding":false},{"id":2125,"name":"Evan E. Eichler","orcid":"0000-0002-8246-4014","position":5,"is_corresponding":false},{"id":19693,"name":"Peter Ebert","orcid":"0000-0001-7441-532X","position":6,"is_corresponding":false},{"id":6321,"name":"Tobias Marschall","orcid":"0000-0002-9376-1030","position":7,"is_corresponding":false},{"id":19705,"name":"Mir Henglin","orcid":"0000-0003-3604-4868","position":0,"is_corresponding":true}],"reference_count":67,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T02:08:32.775003Z","pmid":"38529499","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":[]}