{"doi":"10.1101/2020.07.24.219105","title":"nPhase: An accurate and contiguous phasing method for polyploids","abstract":"Abstract While genome sequencing and assembly are now routine, we still do not have a full and precise picture of polyploid genomes. Phasing these genomes, i.e. deducing haplotypes from genomic data, remains a challenge. Despite numerous attempts, no existing polyploid phasing method provides accurate and contiguous haplotype predictions. To address this need, we developed nPhase, a ploidy agnostic pipeline and algorithm that leverage the accuracy of short reads and the length of long reads to solve reference alignment-based phasing for samples of unspecified ploidy ( https://github.com/nPhasePipeline/nPhase ). nPhase was validated on virtually constructed polyploid genomes of the model species Saccharomyces cerevisiae , generated by combining sequencing data of homozygous isolates. nPhase obtained on average >95% accuracy and a contiguous 1.25 haplotigs per haplotype to cover >90% of each chromosome (heterozygosity rate ≥0.5%). This new phasing method opens the door to explore polyploid genomes through applications such as population genomics and hybrid studies.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2020,"id":122907,"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":4,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9449,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2020-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":564853,"name":"Andreas Tsouris","orcid":"0000-0002-5375-0660","position":1,"is_corresponding":false},{"id":564854,"name":"Anne Friedrich","orcid":"0000-0003-3558-9356","position":2,"is_corresponding":false},{"id":564855,"name":"Joseph Schacherer","orcid":"0000-0002-6606-6884","position":3,"is_corresponding":false},{"id":564852,"name":"Omar Abou Saada","orcid":"0000-0002-5061-0208","position":0,"is_corresponding":true}],"reference_count":30,"raw_metadata":null,"created_at":"2026-07-18T23:14:55.385653Z","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":[]}