{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,15]],"date-time":"2026-03-15T15:50:00Z","timestamp":1773589800452,"version":"3.50.1"},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2026,2,16]],"date-time":"2026-02-16T00:00:00Z","timestamp":1771200000000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100008658","name":"DKFZ","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100008658","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,2,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Commercial solutions like 10X cellranger provide robust UMI quantification for their proprietary single-cell protocols, but open methods such as Smart-seq3 lack comparable support.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Here, we introduce umite, a Smart-seq3 UMI counting pipeline with a focus on speed and a light memory footprint. Unlike existing tools, umite offers efficient mismatch-tolerant UMI detection, boosting UMI retrieval by 5%\u201315% in benchmarks. It also outperforms current Smart-seq3 quantification tools in runtime, disk usage, and memory footprint, offering better scalability on large datasets.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>umite is available at https:\/\/github.com\/leoforster\/umite (or via Zenodo: https:\/\/doi.org\/10.5281\/zenodo.18166431) and includes a Snakemake workflow for Smart-seq3 quantification.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag075","type":"journal-article","created":{"date-parts":[[2026,2,12]],"date-time":"2026-02-12T12:49:23Z","timestamp":1770900563000},"source":"Crossref","is-referenced-by-count":0,"title":["umite: fast quantification of Smart-seq3 libraries with improved UMI retrieval"],"prefix":"10.1093","volume":"42","author":[{"given":"Leo Carl","family":"Foerster","sequence":"first","affiliation":[{"name":"Molecular Neurobiology, German Cancer Research Center (DKFZ) , Heidelberg 69120,","place":["Germany"]},{"name":"Combined Faculty of Mathematics, Engineering and Natural Sciences, University of Heidelberg , Heidelberg 69120,","place":["Germany"]}]},{"given":"Enrico","family":"Frigoli","sequence":"additional","affiliation":[{"name":"Molecular Neurobiology, German Cancer Research Center (DKFZ) , Heidelberg 69120,","place":["Germany"]},{"name":"Combined Faculty of Mathematics, Engineering and Natural Sciences, University of Heidelberg , Heidelberg 69120,","place":["Germany"]}]},{"given":"Xiaoyu","family":"Sun","sequence":"additional","affiliation":[{"name":"Molecular Neurobiology, German Cancer Research Center (DKFZ) , Heidelberg 69120,","place":["Germany"]},{"name":"Combined Faculty of Mathematics, Engineering and Natural Sciences, University of Heidelberg , Heidelberg 69120,","place":["Germany"]}]},{"given":"Jooa","family":"Hooli","sequence":"additional","affiliation":[{"name":"Molecular Neurobiology, German Cancer Research Center (DKFZ) , Heidelberg 69120,","place":["Germany"]},{"name":"Combined Faculty of Mathematics, Engineering and Natural Sciences, University of Heidelberg , Heidelberg 69120,","place":["Germany"]}]},{"given":"Angela","family":"Goncalves","sequence":"additional","affiliation":[{"name":"Computational and Molecular Prevention, German Cancer Research Center (DKFZ) , Heidelberg 69120,","place":["Germany"]},{"name":"DKFZ Hector Cancer Institute, University Medicine Mannheim , Heidelberg 69120,","place":["Germany"]},{"name":"Medical Faculty Mannheim, University of Heidelberg , Heidelberg 69120,","place":["Germany"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9405-8910","authenticated-orcid":false,"given":"Ana","family":"Martin-Villalba","sequence":"additional","affiliation":[{"name":"Molecular Neurobiology, German Cancer Research Center (DKFZ) , Heidelberg 69120,","place":["Germany"]}]}],"member":"286","published-online":{"date-parts":[[2026,2,15]]},"reference":[{"key":"2026031510511818800_btag075-B1","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1093\/bioinformatics\/btu638","article-title":"HTSeq\u2014a python framework to work with high-throughput sequencing data","volume":"31","author":"Anders","year":"2015","journal-title":"Bioinformatics"},{"key":"2026031510511818800_btag075-B2","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1038\/s41586-021-03969-3","article-title":"Isoform cell-type specificity in the mouse primary motor cortex","volume":"598","author":"Booeshaghi","year":"2021","journal-title":"Nature"},{"key":"2026031510511818800_btag075-B3","doi-asserted-by":"publisher","first-page":"496","DOI":"10.1038\/s41586-019-0969-x","article-title":"The single-cell transcriptional landscape of mammalian organogenesis","volume":"566","author":"Cao","year":"2019","journal-title":"Nature"},{"key":"2026031510511818800_btag075-B4","doi-asserted-by":"publisher","first-page":"101555","DOI":"10.1016\/j.xpro.2022.101555","article-title":"High-throughput scNMT protocol for multiomics profiling of single cells from mouse brain and pancreatic organoids","volume":"3","author":"Cerrizuela","year":"2022","journal-title":"STAR Protoc"},{"key":"2026031510511818800_btag075-B5","doi-asserted-by":"publisher","first-page":"1127","DOI":"10.1186\/s12864-024-11036-0","article-title":"Single-Cell sequencing of full-length transcripts and T-Cell receptors with automated high-throughput Smart-Seq3","volume":"25","author":"Chuang","year":"2024","journal-title":"BMC Genomics"},{"key":"2026031510511818800_btag075-B6","doi-asserted-by":"publisher","first-page":"3658","DOI":"10.1038\/s41467-025-58451-9","article-title":"Granulosa cell transcription is similarly impacted by superovulation and aging and predicts early embryonic trajectories","volume":"16","author":"Daugelaite","year":"2025","journal-title":"Nat Commun"},{"key":"2026031510511818800_btag075-B7","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":"2026031510511818800_btag075-B8","doi-asserted-by":"publisher","first-page":"7250","DOI":"10.1038\/s41467-025-62528-w","article-title":"Cross-species comparison reveals therapeutic vulnerabilities halting glioblastoma progression","volume":"16","author":"Foerster","year":"2025","journal-title":"Nat Commun"},{"key":"2026031510511818800_btag075-B9","doi-asserted-by":"publisher","first-page":"708","DOI":"10.1038\/s41587-020-0497-0","article-title":"Single-cell RNA counting at allele and isoform resolution using Smart-Seq3","volume":"38","author":"Hagemann-Jensen","year":"2020","journal-title":"Nat Biotechnol"},{"key":"2026031510511818800_btag075-B10","doi-asserted-by":"publisher","first-page":"449","DOI":"10.1038\/s44161-023-00257-3","article-title":"Three-dimensional morphologic and molecular atlases of nasal vasculature","volume":"2","author":"Hong","year":"2023","journal-title":"Nat Cardiovasc Res"},{"key":"2026031510511818800_btag075-B11","doi-asserted-by":"publisher","first-page":"415","DOI":"10.1038\/s41586-024-07898-9","article-title":"DNA methylation controls stemness of astrocytes in health and ischaemia","volume":"634","author":"Kremer","year":"2024","journal-title":"Nature"},{"key":"2026031510511818800_btag075-B12","author":"McInnes","year":"2020"},{"key":"2026031510511818800_btag075-B13","doi-asserted-by":"publisher","first-page":"1829","DOI":"10.1093\/bioinformatics\/bty888","article-title":"Alignment-free clustering of UMI tagged DNA molecules","volume":"35","author":"Orabi","year":"2019","journal-title":"Bioinformatics"},{"key":"2026031510511818800_btag075-B14","doi-asserted-by":"publisher","first-page":"25533","DOI":"10.1038\/srep25533","article-title":"The impact of amplification on differential expression analyses by RNA-Seq","volume":"6","author":"Parekh","year":"2016","journal-title":"Sci Rep"},{"key":"2026031510511818800_btag075-B15","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1093\/gigascience\/giy059","article-title":"zUMIs\u2014a fast and flexible pipeline to process RNA sequencing data with UMIs","volume":"7","author":"Parekh","year":"2018","journal-title":"Gigascience"},{"key":"2026031510511818800_btag075-B16","doi-asserted-by":"publisher","first-page":"e27041","DOI":"10.7554\/elife.27041","article-title":"The human cell atlas","volume":"6","author":"Regev","year":"2017","journal-title":"Elife"},{"key":"2026031510511818800_btag075-B17","doi-asserted-by":"publisher","first-page":"491","DOI":"10.1101\/gr.209601.116","article-title":"UMI-Tools: modeling sequencing errors in unique molecular identifiers to improve quantification accuracy","volume":"27","author":"Smith","year":"2017","journal-title":"Genome Res"},{"key":"2026031510511818800_btag075-B18","doi-asserted-by":"publisher","first-page":"367","DOI":"10.1038\/s41586-018-0590-4","article-title":"Single-cell transcriptomics of 20 mouse organs creates a tabula muris","volume":"562","author":"The Tabula Muris Consortium, Overall Coordination, Logistical Coordination","year":"2018","journal-title":"Nature"},{"key":"2026031510511818800_btag075-B19","doi-asserted-by":"publisher","first-page":"660366","DOI":"10.3389\/fgene.2021.660366","article-title":"UMIc: a preprocessing method for UMI deduplication and reads correction","volume":"12","author":"Tsagiopoulou","year":"2021","journal-title":"Front Genet"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btag075\/66919560\/btag075.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/42\/3\/btag075\/66919560\/btag075.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/42\/3\/btag075\/66919560\/btag075.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,3,15]],"date-time":"2026-03-15T14:51:24Z","timestamp":1773586284000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btag075\/8487129"}},"subtitle":[],"editor":[{"given":"Can","family":"Alkan","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2026,2,15]]},"references-count":19,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2026,2,28]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btag075","relation":{},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,3]]},"published":{"date-parts":[[2026,2,15]]},"article-number":"btag075"}}