{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T13:48:49Z","timestamp":1782308929468,"version":"3.54.5"},"reference-count":26,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2026,5,21]],"date-time":"2026-05-21T00:00:00Z","timestamp":1779321600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Although RNA-sequencing has replaced microarrays for gene expression profiling over the past 15\u2009years, its full potential for splicing analysis in clinical settings remains underexploited. Most available tools are tailored for large cohorts or known isoforms, limiting their applicability in routine diagnostics where non-recurring events must be identified in low-dimension datasets. We present SAMI (Splicing Analysis with Molecular Indexes), a fully-integrated UMI-aware pipeline designed to detect splicing events diverging from transcript annotations. Building upon the well-proven STAR aligner, SAMI introduces original post-processing of gaps and potential intron retention to maximize accuracy, along with clear graphical representations and tunable filtering stringency. The ability of SAMI and concurrent software to detect intragenic splicing aberrations and gene fusions was assessed, both on real data from a commercial control sample and simulated data generated with ASimulatoR.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Nextflow pipeline and Singularity container recipe freely available under GPL 3 license at https:\/\/github.com\/HCL-HUBL\/SAMI<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag252","type":"journal-article","created":{"date-parts":[[2026,5,18]],"date-time":"2026-05-18T11:20:14Z","timestamp":1779103214000},"source":"Crossref","is-referenced-by-count":0,"title":["Detecting unannotated splicing events in short-read RNA-seq with SAMI, a UMI-aware Nextflow pipeline"],"prefix":"10.1093","volume":"42","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7492-7528","authenticated-orcid":false,"given":"Sylvain","family":"Mareschal","sequence":"first","affiliation":[{"name":"Hospices Civils de Lyon, NGS-HCL plateform, Bioinformatics group , Lyon F-69000,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1331-4549","authenticated-orcid":false,"given":"Valentin","family":"Wucher","sequence":"additional","affiliation":[{"name":"Hospices Civils de Lyon, NGS-HCL plateform, Bioinformatics group , Lyon F-69000,","place":["France"]},{"name":"Hospices Civils de Lyon, French Reference Center of Paraneoplastic Neurological Syndromes and Autoimmune Encephalitis , Lyon F-69000,","place":["France"]},{"name":"Universit\u00e9 Claude Bernard Lyon 1, Mechanisms in integrated life sciences Institute (MeLiS), INSERM U1314, CNRS UMR 5284 , Lyon F-69008,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah","family":"Huet","sequence":"additional","affiliation":[{"name":"Hospices Civils de Lyon, Hematology Department , Lyon F-69000,","place":["France"]},{"name":"Universit\u00e9 Claude Bernard Lyon 1, Centre International de Recherche en Infectiologie, INSERM U1111 \/ CNRS UMR5308, Team Lymphoma Immuno-Biology , Lyon F-69007,","place":["France"]},{"name":"Universit\u00e9 Claude Bernard Lyon 1, Institut des Sciences Pharmaceutiques et Biologiques , Lyon F-69008,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Camille","family":"L\u00e9once","sequence":"additional","affiliation":[{"name":"Hospices Civils de Lyon, Department of Pathology , Lyon F-69000,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kaddour","family":"Chabane","sequence":"additional","affiliation":[{"name":"Hospices Civils de Lyon, Hematology Department , Lyon F-69000,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sandrine","family":"Hayette","sequence":"additional","affiliation":[{"name":"Hospices Civils de Lyon, Hematology Department , Lyon F-69000,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pierre-Paul","family":"Bringuier","sequence":"additional","affiliation":[{"name":"Hospices Civils de Lyon, Department of Pathology , Lyon F-69000,","place":["France"]},{"name":"Universit\u00e9 Claude Bernard Lyon 1 , Villeurbanne F-69100,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"St\u00e9phane","family":"Pinson","sequence":"additional","affiliation":[{"name":"Hospices Civils de Lyon, Genetics department , Lyon F-69000,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3311-4058","authenticated-orcid":false,"given":"Marc","family":"Barritault","sequence":"additional","affiliation":[{"name":"Hospices Civils de Lyon, Department of Pathology , Lyon F-69000,","place":["France"]},{"name":"Universit\u00e9 Claude Bernard Lyon 1, Cancer Research Centre of Lyon (CRCL), INSERM 1052, CNRS 5286, Cancer Initiation and Tumoral Cell Identity Department , Lyon F-69008,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-7197-8730","authenticated-orcid":false,"given":"Claire","family":"Bardel","sequence":"additional","affiliation":[{"name":"Hospices Civils de Lyon, NGS-HCL plateform, Bioinformatics group , Lyon F-69000,","place":["France"]},{"name":"Universit\u00e9 Claude Bernard Lyon 1, Institut des Sciences Pharmaceutiques et Biologiques , Lyon F-69008,","place":["France"]},{"name":"Hospices Civils de Lyon, Genetics department , Lyon F-69000,","place":["France"]},{"name":"Universit\u00e9 Claude Bernard Lyon 1, LBBE, CNRS UMR 5558 , Villeurbanne F-69100,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,5,21]]},"reference":[{"key":"2026062409124205600_btag252-B1","author":"Andrews","year":"2010"},{"key":"2026062409124205600_btag252-B2","doi-asserted-by":"publisher","first-page":"giab007","DOI":"10.1093\/gigascience\/giab007","article-title":"HTSlib: c library for reading\/writing high-throughput sequencing data","volume":"10","author":"Bonfield","year":"2021","journal-title":"Gigascience"},{"key":"2026062409124205600_btag252-B3","doi-asserted-by":"publisher","first-page":"316","DOI":"10.1038\/nbt.3820","article-title":"Nextflow enables reproducible computational workflows","volume":"35","author":"Di Tommaso","year":"2017","journal-title":"Nat Biotechnol"},{"key":"2026062409124205600_btag252-B4","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"2026062409124205600_btag252-B5","doi-asserted-by":"publisher","first-page":"3047","DOI":"10.1093\/bioinformatics\/btw354","article-title":"MultiQC: summarize analysis results for multiple tools and samples in a single report","volume":"32","author":"Ewels","year":"2016","journal-title":"Bioinformatics"},{"key":"2026062409124205600_btag252-B6","doi-asserted-by":"publisher","first-page":"276","DOI":"10.1038\/s41587-020-0439-x","article-title":"The nf-core framework for community-curated bioinformatics pipelines","volume":"38","author":"Ewels","year":"2020","journal-title":"Nat Biotechnol"},{"key":"2026062409124205600_btag252-B7","author":"Fennell","year":"2016"},{"key":"2026062409124205600_btag252-B8","doi-asserted-by":"publisher","first-page":"eaaz5900","DOI":"10.1126\/science.aaz5900","article-title":"Transcriptomic signatures across human tissues identify functional rare genetic variation","volume":"369","author":"Ferraro","year":"2020","journal-title":"Science (New York, N.Y.)"},{"key":"2026062409124205600_btag252-B9","doi-asserted-by":"publisher","first-page":"531","DOI":"10.1186\/s12864-018-4933-1","article-title":"Elimination of PCR duplicates in RNA-seq and small RNA-seq using unique molecular identifiers","volume":"19","author":"Fu","year":"2018","journal-title":"BMC Genomics"},{"key":"2026062409124205600_btag252-B10","doi-asserted-by":"publisher","first-page":"35","DOI":"10.2147\/LCTT.S269307","article-title":"Lung cancer with MET exon 14 skipping mutation: genetic feature, current treatments, and future challenges","volume":"12","author":"Fujino","year":"2021","journal-title":"Lung Cancer (Auckl)"},{"key":"2026062409124205600_btag252-B11","doi-asserted-by":"publisher","first-page":"213","DOI":"10.1186\/s13059-019-1842-9","article-title":"Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods","volume":"20","author":"Haas","year":"2019","journal-title":"Genome Biol"},{"key":"2026062409124205600_btag252-B12","doi-asserted-by":"publisher","first-page":"4609","DOI":"10.1093\/bioinformatics\/btaa259","article-title":"LeafCutterMD: an algorithm for outlier splicing detection in rare diseases","volume":"36","author":"Jenkinson","year":"2020","journal-title":"Bioinformatics"},{"key":"2026062409124205600_btag252-B13","doi-asserted-by":"publisher","first-page":"1634","DOI":"10.1093\/bioinformatics\/btz784","article-title":"SpliceLauncher: a tool for detection, annotation and relative quantification of alternative junctions from RNAseq data","volume":"36","author":"Leman","year":"2020","journal-title":"Bioinformatics"},{"key":"2026062409124205600_btag252-B14","doi-asserted-by":"publisher","first-page":"923","DOI":"10.1093\/bioinformatics\/btt656","article-title":"featureCounts: an efficient general purpose program for assigning sequence reads to genomic features","volume":"30","author":"Liao","year":"2014","journal-title":"Bioinformatics"},{"key":"2026062409124205600_btag252-B15","doi-asserted-by":"publisher","first-page":"3008","DOI":"10.1093\/bioinformatics\/btab142","article-title":"ASimulatoR: splice-aware RNA-Seq data simulation","volume":"37","author":"Manz","year":"2021","journal-title":"Bioinformatics"},{"key":"2026062409124205600_btag252-B16","doi-asserted-by":"publisher","first-page":"2204","DOI":"10.1093\/bioinformatics\/btu185","article-title":"Rgb: a scriptable genome browser for R","volume":"30","author":"Mareschal","year":"2014","journal-title":"Bioinformatics"},{"key":"2026062409124205600_btag252-B17","doi-asserted-by":"publisher","first-page":"10","DOI":"10.14806\/ej.17.1.200","article-title":"Cutadapt removes adapter sequences from high-throughput sequencing reads","volume":"17","author":"Martin","year":"2011","journal-title":"EMBnet j"},{"key":"2026062409124205600_btag252-B18","doi-asserted-by":"publisher","author":"Nicorici","year":"2014","DOI":"10.1101\/011650"},{"key":"2026062409124205600_btag252-B19","author":"Renevey","year":"2024"},{"key":"2026062409124205600_btag252-B20","doi-asserted-by":"publisher","first-page":"2056","DOI":"10.1016\/j.ajhg.2023.10.014","article-title":"Improved detection of aberrant splicing with FRASER 2.0 and the intron Jaccard index","volume":"110","author":"Scheller","year":"2023","journal-title":"Am J Hum Genet"},{"key":"2026062409124205600_btag252-B21","doi-asserted-by":"publisher","first-page":"88","DOI":"10.1186\/s13104-016-1900-2","article-title":"AdapterRemoval v2: rapid adapter trimming, identification, and read merging","volume":"9","author":"Schubert","year":"2016","journal-title":"BMC Res Notes"},{"key":"2026062409124205600_btag252-B22","doi-asserted-by":"publisher","first-page":"E5593","DOI":"10.1073\/pnas.1419161111","article-title":"rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-seq data","volume":"111","author":"Shen","year":"2014","journal-title":"Proc Nat Acad Sci U S A"},{"key":"2026062409124205600_btag252-B23","doi-asserted-by":"publisher","first-page":"40","DOI":"10.1186\/s13059-018-1417-1","article-title":"SUPPA2: fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions","volume":"19","author":"Trincado","year":"2018","journal-title":"Genome Biol"},{"key":"2026062409124205600_btag252-B24","doi-asserted-by":"publisher","first-page":"448","DOI":"10.1101\/gr.257246.119","article-title":"Accurate and efficient detection of gene fusions from RNA sequencing data","volume":"31","author":"Uhrig","year":"2021","journal-title":"Genome Res"},{"key":"2026062409124205600_btag252-B25","doi-asserted-by":"publisher","first-page":"1230","DOI":"10.1038\/s41467-023-36585-y","article-title":"RNA splicing analysis using heterogeneous and large RNA-seq datasets","volume":"14","author":"Vaquero-Garcia","year":"2023","journal-title":"Nat Commun"},{"key":"2026062409124205600_btag252-B26","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1093\/bioinformatics\/btv642","article-title":"Two-pass alignment improves novel splice junction quantification","volume":"32","author":"Veeneman","year":"2016","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btag252\/68363709\/btag252.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/42\/6\/btag252\/68363709\/btag252.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/42\/6\/btag252\/68363709\/btag252.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T13:12:48Z","timestamp":1782306768000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btag252\/8690164"}},"subtitle":[],"editor":[{"given":"Can","family":"Alkan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,5,21]]},"references-count":26,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2026,6,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btag252","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,6]]},"published":{"date-parts":[[2026,5,21]]},"article-number":"btag252"}}