{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,15]],"date-time":"2026-03-15T07:32:55Z","timestamp":1773559975604,"version":"3.50.1"},"reference-count":29,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2025,9,4]],"date-time":"2025-09-04T00:00:00Z","timestamp":1756944000000},"content-version":"vor","delay-in-days":3,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Civitan International Research Center"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Recent advancements in long-read single-cell RNA sequencing (scRNA-seq) have facilitated the quantification of full-length transcripts and isoforms at the single-cell level. Historically, long-read data would need to be complemented with short-read single-cell data in order to overcome the higher sequencing errors to correctly identify cellular barcodes and unique molecular identifiers. Improvements in Oxford Nanopore sequencing, and development of novel computational methods have removed this requirement. Though these methods now exist, the limited availability of modular and portable workflows remains a challenge.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Here, we present, nf-core\/scnanoseq, a secondary analysis pipeline for long-read single-cell and single-nuclei RNA that delivers gene and transcript-level quantification. The scnanoseq pipeline is implemented using Nextflow and is built upon the nf-core framework, enabling portability across computational environments, scalability and reproducibility of results across pipeline runs. The nf-core\/scnanoseq workflow follows best practices for analyzing single-cell and single-nuclei data, performing barcode detection and correction, genome and transcriptome read alignment, unique molecular identifier deduplication, gene and transcript quantification, and extensive quality control reporting.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The source code, and detailed documentation are freely available at https:\/\/github.com\/nf-core\/scnanoseq and https:\/\/nf-co.re\/scnanoseq under the MIT License. Documentation for the version of nf-core\/scnanoseq used for this paper, including default parameters and descriptions of output files are available at https:\/\/nf-co.re\/scnanoseq\/1.1.0<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf487","type":"journal-article","created":{"date-parts":[[2025,9,3]],"date-time":"2025-09-03T11:42:17Z","timestamp":1756899737000},"source":"Crossref","is-referenced-by-count":1,"title":["scnanoseq: an nf-core pipeline for Oxford Nanopore single-cell RNA-sequencing"],"prefix":"10.1093","volume":"41","author":[{"given":"Austyn","family":"Trull","sequence":"first","affiliation":[{"name":"Institutional Research Core Program\u2014Biological Data Science Core, University of Alabama at Birmingham , Birmingham, AL, 35233,","place":["United States"]}]},{"given":"Elizabeth A","family":"Worthey","sequence":"additional","affiliation":[{"name":"Institutional Research Core Program\u2014Biological Data Science Core, University of Alabama at Birmingham , Birmingham, AL, 35233,","place":["United States"]},{"name":"Department of Genetics, University of Alabama at Birmingham , Birmingham, AL, 35233,","place":["United States"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1859-2118","authenticated-orcid":false,"given":"Lara","family":"Ianov","sequence":"additional","affiliation":[{"name":"Institutional Research Core Program\u2014Biological Data Science Core, University of Alabama at Birmingham , Birmingham, AL, 35233,","place":["United States"]},{"name":"Department of Neurobiology, University of Alabama at Birmingham , Birmingham, AL, 35233,","place":["United States"]}]}],"member":"286","published-online":{"date-parts":[[2025,9,4]]},"reference":[{"key":"2025091923393587800_btaf487-B1","author":"10x Genomics","year":"2022"},{"key":"2025091923393587800_btaf487-B2","author":"10x Genomics","year":"2022"},{"key":"2025091923393587800_btaf487-B3","author":"10x Genomics","year":"2022"},{"key":"2025091923393587800_btaf487-B4","author":"Andrews","year":"2010"},{"key":"2025091923393587800_btaf487-B5","author":"Broad Institute","year":"2019"},{"key":"2025091923393587800_btaf487-B6","doi-asserted-by":"crossref","first-page":"16027","DOI":"10.1038\/ncomms16027","article-title":"Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual b cells","volume":"8","author":"Byrne","year":"2017","journal-title":"Nat Commun"},{"key":"2025091923393587800_btaf487-B7","doi-asserted-by":"crossref","first-page":"2666","DOI":"10.1093\/bioinformatics\/bty149","article-title":"NanoPack: visualizing and processing long-read sequencing data","volume":"34","author":"De Coster","year":"2018","journal-title":"Bioinformatics"},{"key":"2025091923393587800_btaf487-B8","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btad311","article-title":"NanoPack2: population-scale evaluation of long-read sequencing data","volume":"39","author":"De Coster","year":"2023","journal-title":"Bioinformatics"},{"key":"2025091923393587800_btaf487-B9","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btae549","article-title":"Scywalker: scalable end-to-end data analysis workflow for long-read single-cell transcriptome sequencing","volume":"40","author":"De Rijk","year":"2024","journal-title":"Bioinformatics"},{"key":"2025091923393587800_btaf487-B10","doi-asserted-by":"crossref","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":"2025091923393587800_btaf487-B11","author":"Dias","year":"2024"},{"key":"2025091923393587800_btaf487-B12","doi-asserted-by":"crossref","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":"2025091923393587800_btaf487-B13","doi-asserted-by":"crossref","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":"2025091923393587800_btaf487-B14","doi-asserted-by":"crossref","first-page":"1197","DOI":"10.1038\/nbt.4259","article-title":"Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells","volume":"36","author":"Gupta","year":"2018","journal-title":"Nat Biotechnol"},{"key":"2025091923393587800_btaf487-B15","doi-asserted-by":"crossref","first-page":"3573","DOI":"10.1016\/j.cell.2021.04.048","article-title":"Integrated analysis of multimodal single-cell data","volume":"184","author":"Hao","year":"2021","journal-title":"Cell"},{"key":"2025091923393587800_btaf487-B16","doi-asserted-by":"crossref","first-page":"i304","DOI":"10.1093\/bioinformatics\/btaf240","article-title":"Oarfish: enhanced probabilistic modeling leads to improved accuracy in long read transcriptome quantification","volume":"41","author":"Jousheghani","year":"2025","journal-title":"Bioinformatics"},{"key":"2025091923393587800_btaf487-B17","doi-asserted-by":"crossref","first-page":"1005","DOI":"10.1007\/s00439-024-02678-x","article-title":"Advances in long-read single-cell transcriptomics","volume":"143","author":"Kumari","year":"2024","journal-title":"Hum Genet"},{"key":"2025091923393587800_btaf487-B18","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1186\/s13059-025-03673-9","article-title":"Empowering bioinformatics communities with nextflow and nf-core","volume":"26","author":"Langer","year":"2025","journal-title":"Genome Biol"},{"key":"2025091923393587800_btaf487-B19","doi-asserted-by":"crossref","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","article-title":"Minimap2: pairwise alignment for nucleotide sequences","volume":"34","author":"Li","year":"2018","journal-title":"Bioinformatics"},{"key":"2025091923393587800_btaf487-B20","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2025091923393587800_btaf487-B21","article-title":"Long-read sequencing transcriptome quantification with lr-kallisto","author":"Loving","year":"2025"},{"key":"2025091923393587800_btaf487-B22","author":"Oxford Nanopore Technologies","year":"2024"},{"key":"2025091923393587800_btaf487-B23","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":"2025091923393587800_btaf487-B24","doi-asserted-by":"crossref","first-page":"2631","DOI":"10.1038\/s41467-023-38324-9","article-title":"High-throughput and high-accuracy single-cell RNA isoform analysis using PacBio circular consensus sequencing","volume":"14","author":"Shi","year":"2023","journal-title":"Nat Commun"},{"key":"2025091923393587800_btaf487-B25","doi-asserted-by":"crossref","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":"2025091923393587800_btaf487-B26","doi-asserted-by":"crossref","first-page":"310","DOI":"10.1186\/s13059-021-02525-6","article-title":"Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing","volume":"22","author":"Tian","year":"2021","journal-title":"Genome Biol"},{"key":"2025091923393587800_btaf487-B27","doi-asserted-by":"crossref","first-page":"2184","DOI":"10.1093\/bioinformatics\/bts356","article-title":"RSeQC: quality control of RNA-seq experiments","volume":"28","author":"Wang","year":"2012","journal-title":"Bioinformatics"},{"key":"2025091923393587800_btaf487-B28","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1186\/s13059-017-1382-0","article-title":"SCANPY: large-scale single-cell gene expression data analysis","volume":"19","author":"Wolf","year":"2018","journal-title":"Genome Biol"},{"key":"2025091923393587800_btaf487-B29","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1186\/s13059-023-02907-y","article-title":"Identification of cell barcodes from long-read single-cell RNA-seq with BLAZE","volume":"24","author":"You","year":"2023","journal-title":"Genome Biol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaf487\/64208982\/btaf487.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/41\/9\/btaf487\/64208982\/btaf487.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/41\/9\/btaf487\/64208982\/btaf487.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,9,20]],"date-time":"2025-09-20T03:39:48Z","timestamp":1758339588000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btaf487\/8247965"}},"subtitle":[],"editor":[{"given":"Peter","family":"Robinson","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2025,9,1]]},"references-count":29,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2025,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaf487","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2025.04.08.647887","asserted-by":"object"}]},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025,9]]},"published":{"date-parts":[[2025,9,1]]},"article-number":"btaf487"}}