{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,15]],"date-time":"2026-03-15T07:32:52Z","timestamp":1773559972630,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1013692","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2025,12,5]],"date-time":"2025-12-05T00:00:00Z","timestamp":1764892800000}}],"reference-count":46,"publisher":"Public Library of Science (PLoS)","issue":"12","license":[{"start":{"date-parts":[[2025,12,1]],"date-time":"2025-12-01T00:00:00Z","timestamp":1764547200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100006192","name":"Advanced Scientific Computing Research","doi-asserted-by":"publisher","award":["DE-SC0020347"],"award-info":[{"award-number":["DE-SC0020347"]}],"id":[{"id":"10.13039\/100006192","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006652","name":"National Center for Institutional Diversity, University of Michigan","doi-asserted-by":"publisher","award":["HG012077"],"award-info":[{"award-number":["HG012077"]}],"id":[{"id":"10.13039\/100006652","id-type":"DOI","asserted-by":"publisher"}]},{"name":"NIH NIGMS","award":["T32 GM008042"],"award-info":[{"award-number":["T32 GM008042"]}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>RNA abundance quantification has become routine and affordable thanks to high-throughput \u201cshort-read\u201d 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. \u201cLong-read\u201d 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.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1013692","type":"journal-article","created":{"date-parts":[[2025,12,1]],"date-time":"2025-12-01T18:49:08Z","timestamp":1764614948000},"page":"e1013692","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":5,"title":["Long-read sequencing transcriptome quantification with lr-kallisto"],"prefix":"10.1371","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8725-0376","authenticated-orcid":true,"given":"Rebekah K.","family":"Loving","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8359-6705","authenticated-orcid":true,"given":"Delaney K.","family":"Sullivan","sequence":"additional","affiliation":[]},{"given":"Fairlie","family":"Reese","sequence":"additional","affiliation":[]},{"given":"Elisabeth","family":"Rebboah","sequence":"additional","affiliation":[]},{"given":"Jasmine","family":"Sakr","sequence":"additional","affiliation":[]},{"given":"Narges","family":"Rezaie","sequence":"additional","affiliation":[]},{"given":"Heidi Y.","family":"Liang","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2612-2554","authenticated-orcid":true,"given":"Ghassan","family":"Filimban","sequence":"additional","affiliation":[]},{"given":"Shimako","family":"Kawauchi","sequence":"additional","affiliation":[]},{"given":"A. 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