{"doi":"10.1101/2021.03.26.437240","title":"Haplotype-aware pantranscriptome analyses using spliced pangenome graphs","abstract":"Abstract Pangenomics is emerging as a powerful computational paradigm in bioinformatics. This field uses population-level genome reference structures, typically consisting of a sequence graph, to mitigate reference bias and facilitate analyses that were challenging with previous reference-based methods. In this work, we extend these methods into transcriptomics to analyze sequencing data using the pantranscriptome: a population-level transcriptomic reference. Our novel toolchain can construct spliced pangenome graphs, map RNA-seq data to these graphs, and perform haplotype-aware expression quantification of transcripts in a pantranscriptome. This workflow improves accuracy over state-of-the-art RNA-seq mapping methods, and it can efficiently quantify haplotype-specific transcript expression without needing to characterize a sample’s haplotypes beforehand.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2021,"id":213584,"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":18,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9518,"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":6318,"name":"Jordan M. Eizenga","orcid":"0000-0001-8345-8356","position":1,"is_corresponding":false},{"id":109821,"name":"Adam M. Novak","orcid":"0000-0001-5828-047X","position":2,"is_corresponding":false},{"id":24549,"name":"Jouni Sirén","orcid":"0000-0001-5828-4139","position":3,"is_corresponding":false},{"id":231855,"name":"Xian Chang","orcid":"0000-0002-3801-4542","position":4,"is_corresponding":false},{"id":109462,"name":"Erik Garrison","orcid":"0000-0003-3821-631X","position":5,"is_corresponding":false},{"id":108063,"name":"Benedict Paten","orcid":"0000-0001-8863-3539","position":6,"is_corresponding":false},{"id":30906,"name":"Jonas A. Sibbesen","orcid":"0000-0002-5528-0236","position":0,"is_corresponding":true}],"reference_count":98,"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":[]}