{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:22Z","timestamp":1772138062792,"version":"3.50.1"},"reference-count":23,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2024,1,23]],"date-time":"2024-01-23T00:00:00Z","timestamp":1705968000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"NIGMS Maximizing Investigators\u2019 Research Award","award":["R35 GM138152"],"award-info":[{"award-number":["R35 GM138152"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Recent advancements in long-read RNA sequencing have enabled the examination of full-length isoforms, previously uncaptured by short-read sequencing methods. An alternative powerful method for studying isoforms is through the use of barcoded short-read RNA reads, for which a barcode indicates whether two short-reads arise from the same molecule or not. Such techniques included the 10x Genomics linked-read based SParse Isoform Sequencing (SPIso-seq), as well as Loop-Seq, or Tell-Seq. Some applications, such as novel-isoform discovery, require very high coverage. Obtaining high coverage using long reads can be difficult, making barcoded RNA-seq data a valuable alternative for this task. However, most annotation pipelines are not able to work with a set of short reads instead of a single transcript, also not able to work with coverage gaps within a molecule if any. In order to overcome this challenge, we present an RNA-seq assembler that allows the determination of the expressed isoform per barcode.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>In this article, we present cloudrnaSPAdes, a tool for assembling full-length isoforms from barcoded RNA-seq linked-read data in a reference-free fashion. Evaluating it on simulated and real human data, we found that cloudrnaSPAdes accurately assembles isoforms, even for genes with high isoform diversity.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>cloudrnaSPAdes is a feature release of a SPAdes assembler and version used for this article is available at https:\/\/github.com\/1dayac\/cloudrnaSPAdes-release.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad781","type":"journal-article","created":{"date-parts":[[2024,1,18]],"date-time":"2024-01-18T15:16:39Z","timestamp":1705590999000},"source":"Crossref","is-referenced-by-count":0,"title":["<scp>cloudrna<\/scp>\n                    SP\n                    <scp>Ades<\/scp>\n                    : isoform assembly using bulk barcoded RNA sequencing data"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7398-9820","authenticated-orcid":false,"given":"Dmitry","family":"Meleshko","sequence":"first","affiliation":[{"name":"Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine of Cornell University , New York, NY 10021, United States"},{"name":"Department of Physiology and Biophysics, Institute for Computational Biomedicine, Weill Cornell Medicine , New York, NY 10021, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrey D","family":"Prjbelski","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Helsinki , Helsinki 00014, Finland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mikhail","family":"Raiko","sequence":"additional","affiliation":[{"name":"Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St Petersburg State University , St Petersburg 199004, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5747-8350","authenticated-orcid":false,"given":"Alexandru I","family":"Tomescu","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Helsinki , Helsinki 00014, Finland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7058-3606","authenticated-orcid":false,"given":"Hagen","family":"Tilgner","sequence":"additional","affiliation":[{"name":"Brain and Mind Research Institute, Weill Cornell Medicine , New York, NY 10021, United States"},{"name":"Center for Neurogenetics, Weill Cornell Medicine , New York, NY 10021, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0600-3371","authenticated-orcid":false,"given":"Iman","family":"Hajirasouliha","sequence":"additional","affiliation":[{"name":"Department of Physiology and Biophysics, Institute for Computational Biomedicine, Weill Cornell Medicine , New York, NY 10021, United States"},{"name":"Englander Institute for Precision Medicine, The Meyer Cancer Center, Weill Cornell Medicine , New York, NY 10021, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2024,1,23]]},"reference":[{"key":"2024020805382286000_btad781-B1","doi-asserted-by":"crossref","first-page":"E4821","DOI":"10.1073\/pnas.1320101110","article-title":"Characterization of the human ESC transcriptome by hybrid sequencing","volume":"110","author":"Au","year":"2013","journal-title":"Proc Natl Acad Sci USA"},{"key":"2024020805382286000_btad781-B2","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing","volume":"19","author":"Bankevich","year":"2012","journal-title":"J Comput Biol"},{"key":"2024020805382286000_btad781-B3","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1038\/nmeth.3737","article-title":"TruSPAdes: barcode assembly of TruSeq synthetic long reads","volume":"13","author":"Bankevich","year":"2016","journal-title":"Nat Methods"},{"key":"2024020805382286000_btad781-B4","doi-asserted-by":"crossref","first-page":"giz100","DOI":"10.1093\/gigascience\/giz100","article-title":"rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data","volume":"8","author":"Bushmanova","year":"2019","journal-title":"Gigascience"},{"key":"2024020805382286000_btad781-B5","doi-asserted-by":"crossref","first-page":"130","DOI":"10.1186\/s40168-021-01072-3","article-title":"Ultra-accurate microbial amplicon sequencing with synthetic long reads","volume":"9","author":"Callahan","year":"2021","journal-title":"Microbiome"},{"key":"2024020805382286000_btad781-B6","doi-asserted-by":"crossref","first-page":"898","DOI":"10.1101\/gr.260380.119","article-title":"Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information","volume":"30","author":"Chen","year":"2020","journal-title":"Genome Res"},{"key":"2024020805382286000_btad781-B7","doi-asserted-by":"crossref","first-page":"R80","DOI":"10.1186\/gb-2004-5-10-r80","article-title":"Bioconductor: open software development for computational biology and bioinformatics","volume":"5","author":"Gentleman","year":"2004","journal-title":"Genome Biol"},{"key":"2024020805382286000_btad781-B8","doi-asserted-by":"crossref","first-page":"521","DOI":"10.1093\/bioinformatics\/bty630","article-title":"Simulating Illumina metagenomic data with InSilicoSeq","volume":"35","author":"Gourl\u00e9","year":"2019","journal-title":"Bioinformatics"},{"key":"2024020805382286000_btad781-B9","doi-asserted-by":"crossref","first-page":"644","DOI":"10.1038\/nbt.1883","article-title":"Full-length transcriptome assembly from RNA-Seq data without a reference genome","volume":"29","author":"Grabherr","year":"2011","journal-title":"Nat Biotechnol"},{"key":"2024020805382286000_btad781-B10","doi-asserted-by":"crossref","first-page":"105922","DOI":"10.1016\/j.phrs.2021.105922","article-title":"Functions of the (pro) renin receptor (Atp6ap2) at molecular and system levels: pathological implications in hypertension, renal and brain development, inflammation, and fibrosis","volume":"173","author":"Hoffmann","year":"2021","journal-title":"Pharmacol Res"},{"key":"2024020805382286000_btad781-B11","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12864-020-07123-7","article-title":"Illuminating the dark side of the human transcriptome with long read transcript sequencing","volume":"21","author":"Kuo","year":"2020","journal-title":"BMC Genomics"},{"key":"2024020805382286000_btad781-B12","doi-asserted-by":"crossref","first-page":"1191","DOI":"10.1101\/gr.260174.119","article-title":"RNA-Bloom enables reference-free and reference-guided sequence assembly for single-cell transcriptomes","volume":"30","author":"Nip","year":"2020","journal-title":"Genome Res"},{"key":"2024020805382286000_btad781-B13","doi-asserted-by":"crossref","first-page":"714","DOI":"10.1089\/cmb.2013.0084","article-title":"Assembling single-cell genomes and mini-metagenomes from chimeric MDA products","volume":"20","author":"Nurk","year":"2013","journal-title":"J Comput Biol"},{"key":"2024020805382286000_btad781-B14","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1038\/nbt.3122","article-title":"StringTie enables improved reconstruction of a transcriptome from RNA-seq reads","volume":"33","author":"Pertea","year":"2015","journal-title":"Nat Biotechnol"},{"key":"2024020805382286000_btad781-B15","doi-asserted-by":"crossref","first-page":"e102","DOI":"10.1002\/cpbi.102","article-title":"Using SPAdes de novo assembler","volume":"70","author":"Prjibelski","year":"2020","journal-title":"Curr Protoc Bioinformatics"},{"key":"2024020805382286000_btad781-B16","doi-asserted-by":"crossref","first-page":"915","DOI":"10.1038\/s41587-022-01565-y","article-title":"Accurate isoform discovery with IsoQuant using long reads","volume":"41","author":"Prjibelski","year":"2023","journal-title":"Nat Biotechnol"},{"key":"2024020805382286000_btad781-B17","doi-asserted-by":"crossref","first-page":"i293","DOI":"10.1093\/bioinformatics\/btu266","article-title":"ExSPAnder: a universal repeat resolver for DNA fragment assembly","volume":"30","author":"Prjibelski","year":"2014","journal-title":"Bioinformatics"},{"key":"2024020805382286000_btad781-B18","doi-asserted-by":"crossref","first-page":"1009","DOI":"10.1038\/nbt.2705","article-title":"A single-molecule long-read survey of the human transcriptome","volume":"31","author":"Sharon","year":"2013","journal-title":"Nat Biotechnol"},{"key":"2024020805382286000_btad781-B19","doi-asserted-by":"crossref","first-page":"1438","DOI":"10.1038\/s41467-020-15171-6","article-title":"Full-length transcript characterization of SF3B1 mutation in chronic lymphocytic leukemia reveals downregulation of retained introns","volume":"11","author":"Tang","year":"2020","journal-title":"Nat Commun"},{"key":"2024020805382286000_btad781-B20","doi-asserted-by":"crossref","first-page":"9869","DOI":"10.1073\/pnas.1400447111","article-title":"Defining a personal, allele-specific, and single-molecule long-read transcriptome","volume":"111","author":"Tilgner","year":"2014","journal-title":"Proc Natl Acad Sci USA"},{"key":"2024020805382286000_btad781-B21","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1101\/gr.230516.117","article-title":"Microfluidic isoform sequencing shows widespread splicing coordination in the human transcriptome","volume":"28","author":"Tilgner","year":"2018","journal-title":"Genome Res"},{"key":"2024020805382286000_btad781-B22","doi-asserted-by":"crossref","first-page":"i61","DOI":"10.1093\/bioinformatics\/btz349","article-title":"cloudSPAdes: assembly of synthetic long reads using de Bruijn graphs","volume":"35","author":"Tolstoganov","year":"2019","journal-title":"Bioinformatics"},{"key":"2024020805382286000_btad781-B23","doi-asserted-by":"crossref","first-page":"3350","DOI":"10.1093\/bioinformatics\/btv383","article-title":"Bandage: interactive visualization of de novo genome assemblies","volume":"31","author":"Wick","year":"2015","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btad781\/56345516\/btad781.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/40\/2\/btad781\/56619426\/btad781.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/40\/2\/btad781\/56619426\/btad781.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,2,8]],"date-time":"2024-02-08T01:03:18Z","timestamp":1707354198000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btad781\/7585775"}},"subtitle":[],"editor":[{"given":"Christina","family":"Kendziorski","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2024,1,23]]},"references-count":23,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2024,2,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btad781","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2023.07.25.550587","asserted-by":"object"}]},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2024,2,1]]},"published":{"date-parts":[[2024,1,23]]},"article-number":"btad781"}}