{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:31Z","timestamp":1772138071430,"version":"3.50.1"},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:00:00Z","timestamp":1740182400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"France G\u00e9nomique national infrastructure"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,3,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>The combination of long-read sequencing technologies like Oxford Nanopore with single-cell RNA sequencing (scRNAseq) assays enables the detailed exploration of transcriptomic complexity, including isoform detection and quantification, by capturing full-length cDNAs. However, challenges remain, including the lack of advanced simulation tools that can effectively mimic the unique complexities of scRNAseq long-read datasets. Such tools are essential for the evaluation and optimization of isoform detection methods dedicated to single-cell long-read studies.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We developed AsaruSim, a workflow that simulates synthetic single-cell long-read Nanopore datasets, closely mimicking real experimental data. AsaruSim employs a multi-step process that includes the creation of a synthetic count matrix, generation of perfect reads, optional PCR amplification, introduction of sequencing errors, and comprehensive quality control reporting. Applied to a dataset of human peripheral blood mononuclear cells, AsaruSim accurately reproduced experimental read characteristics.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The source code and full documentation are available at https:\/\/github.com\/GenomiqueENS\/AsaruSim.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf087","type":"journal-article","created":{"date-parts":[[2025,2,20]],"date-time":"2025-02-20T07:17:42Z","timestamp":1740035862000},"source":"Crossref","is-referenced-by-count":2,"title":["AsaruSim: a single-cell and spatial RNA-Seq Nanopore long-reads simulation workflow"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0009-0008-7001-4252","authenticated-orcid":false,"given":"Ali","family":"Hamraoui","sequence":"first","affiliation":[{"name":"GenomiqueENS, Institut de Biologie de l\u2019ENS (IBENS), D\u00e9partement de biologie, \u00c9cole normale sup\u00e9rieure, CNRS, INSERM, Universit\u00e9 PSL , Paris 75005,","place":["France"]},{"name":"Group Bacterial Infection, Response & Dynamics, Institut de biologie de l\u2019ENS (IBENS), \u00c9cole normale sup\u00e9rieure, CNRS, INSERM, Universit\u00e9 PSL , Paris 75005,","place":["France"]}]},{"given":"Laurent","family":"Jourdren","sequence":"additional","affiliation":[{"name":"GenomiqueENS, Institut de Biologie de l\u2019ENS (IBENS), D\u00e9partement de biologie, \u00c9cole normale sup\u00e9rieure, CNRS, INSERM, Universit\u00e9 PSL , Paris 75005,","place":["France"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2608-476X","authenticated-orcid":false,"given":"Morgane","family":"Thomas-Chollier","sequence":"additional","affiliation":[{"name":"GenomiqueENS, Institut de Biologie de l\u2019ENS (IBENS), D\u00e9partement de biologie, \u00c9cole normale sup\u00e9rieure, CNRS, INSERM, Universit\u00e9 PSL , Paris 75005,","place":["France"]},{"name":"Group Bacterial Infection, Response & Dynamics, Institut de biologie de l\u2019ENS (IBENS), \u00c9cole normale sup\u00e9rieure, CNRS, INSERM, Universit\u00e9 PSL , Paris 75005,","place":["France"]}]}],"member":"286","published-online":{"date-parts":[[2025,2,22]]},"reference":[{"key":"2025031206274316900_btaf087-B1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13059-018-1496-z","article-title":"Single-cell RNAseq for the study of isoforms\u2014how is that possible?","volume":"19","author":"Arzalluz-Luque","year":"2018","journal-title":"Genome Biol"},{"key":"2025031206274316900_btaf087-B2","doi-asserted-by":"crossref","first-page":"1468","DOI":"10.1093\/bioinformatics\/btz752","article-title":"SPARSim single cell: a count data simulator for scRNA-Seq 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