{"doi":"10.1101/2024.07.19.604364","title":"Long-read sequencing transcriptome quantification with lr-kallisto","abstract":"RNA abundance quantification has become routine and affordable thanks to high-throughput \"short-read\" technologies that provide accurate molecule counts at the gene level. Similarly accurate and affordable quantification of definitive full-length, transcript isoforms has remained a stubborn challenge, despite its obvious biological significance across a wide range of problems. \"Long-read\" sequencing platforms now produce data-types that can, in principle, drive routine definitive isoform quantification. However some particulars of contemporary long-read datatypes, together with isoform complexity and genetic variation, present bioinformatic challenges. We show here, using ONT data, that fast and accurate quantification of long-read data is possible and that it is improved by exome capture. To perform quantifications we developed lr-kallisto, which adapts the kallisto bulk and single-cell RNA-seq quantification methods for long-read technologies.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2024,"id":484184,"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":0.8716,"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":387782,"name":"Delaney K. Sullivan","orcid":"0000-0002-8359-6705","position":1,"is_corresponding":false},{"id":58987,"name":"A. Sina Booeshaghi","orcid":"0000-0002-6442-4502","position":2,"is_corresponding":false},{"id":479159,"name":"Fairlie Reese","orcid":"0000-0002-9240-0102","position":3,"is_corresponding":false},{"id":653818,"name":"Elisabeth Rebboah","orcid":"0000-0003-2273-0189","position":4,"is_corresponding":false},{"id":1009828,"name":"Jasmine Sakr","orcid":"0000-0002-4470-3192","position":5,"is_corresponding":false},{"id":812207,"name":"Narges Rezaie","orcid":"0000-0001-9326-9954","position":6,"is_corresponding":false},{"id":653819,"name":"Heidi Yahan Liang","orcid":"0000-0002-6190-9723","position":7,"is_corresponding":false},{"id":1029883,"name":"Ghassan Filimban","orcid":"0000-0002-2612-2554","position":8,"is_corresponding":false},{"id":812204,"name":"Shimako Kawauchi","orcid":"0000-0002-8577-4763","position":9,"is_corresponding":false},{"id":1060753,"name":"Conrad Oakes","orcid":"0000-0002-8936-055X","position":10,"is_corresponding":false},{"id":11778,"name":"Diane Trout","orcid":"0000-0002-4928-5532","position":11,"is_corresponding":false},{"id":11729,"name":"Brian A. Williams","orcid":"0000-0003-3253-611X","position":12,"is_corresponding":false},{"id":459925,"name":"Grant R. MacGregor","orcid":"0000-0001-7598-9501","position":13,"is_corresponding":false},{"id":11810,"name":"Barbara Wold","orcid":"0000-0003-3235-8130","position":14,"is_corresponding":false},{"id":11794,"name":"Ali Mortazavi","orcid":"0000-0002-4259-6362","position":15,"is_corresponding":false},{"id":242923,"name":"Lior Pachter","orcid":"0000-0002-9164-6231","position":16,"is_corresponding":false},{"id":1325804,"name":"Rebekah K. Loving","orcid":"0000-0001-8725-0376","position":0,"is_corresponding":true}],"reference_count":47,"raw_metadata":null,"created_at":"2026-07-19T02:07:38.055693Z","pmid":"39071335","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":[]}