{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:43:31Z","timestamp":1753875811138,"version":"3.41.2"},"reference-count":21,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2023,9,22]],"date-time":"2023-09-22T00:00:00Z","timestamp":1695340800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2022YFC3400400"],"award-info":[{"award-number":["2022YFC3400400"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32170644","32250710678"],"award-info":[{"award-number":["32170644","32250710678"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Shenzhen Science and Technology Program","award":["JCYJ20220530115211026","202208183000231"],"award-info":[{"award-number":["JCYJ20220530115211026","202208183000231"]}]},{"name":"Shenzhen Innovation Committee of Science and Technology","award":["ZDSYS20200811144002008"],"award-info":[{"award-number":["ZDSYS20200811144002008"]}]},{"DOI":"10.13039\/501100021171","name":"Guangdong Basic and Applied Basic Research Foundation","doi-asserted-by":"publisher","award":["2023A1515011231"],"award-info":[{"award-number":["2023A1515011231"]}],"id":[{"id":"10.13039\/501100021171","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,9,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Single-cell multiomics techniques have been widely applied to detect the key signature of cells. These methods have achieved a single-molecule resolution and can even reveal spatial localization. These emerging methods provide insights elucidating the features of genomic, epigenomic and transcriptomic heterogeneity in individual cells. However, they have given rise to new computational challenges in data processing. Here, we describe Single-cell Single-molecule multiple Omics Pipeline (ScSmOP), a universal pipeline for barcode-indexed single-cell single-molecule multiomics data analysis. Essentially, the C language is utilized in ScSmOP to set up spaced-seed hash table-based algorithms for barcode identification according to ligation-based barcoding data and synthesis-based barcoding data, followed by data mapping and deconvolution. We demonstrate high reproducibility of data processing between ScSmOP and published pipelines in comprehensive analyses of single-cell omics data (scRNA-seq, scATAC-seq, scARC-seq), single-molecule chromatin interaction data (ChIA-Drop, SPRITE, RD-SPRITE), single-cell single-molecule chromatin interaction data (scSPRITE) and spatial transcriptomic data from various cell types and species. Additionally, ScSmOP shows more rapid performance and is a versatile, efficient, easy-to-use and robust pipeline for single-cell single-molecule multiomics data analysis.<\/jats:p>","DOI":"10.1093\/bib\/bbad343","type":"journal-article","created":{"date-parts":[[2023,10,2]],"date-time":"2023-10-02T04:01:30Z","timestamp":1696219290000},"source":"Crossref","is-referenced-by-count":1,"title":["ScSmOP: a universal computational pipeline for single-cell single-molecule multiomics data analysis"],"prefix":"10.1093","volume":"24","author":[{"given":"Kai","family":"Jing","sequence":"first","affiliation":[{"name":"Shenzhen Key Laboratory of Gene Regulation and Systems Biology , School of Life Sciences, , Shenzhen 518055, China"},{"name":"Southern University of Science and Technology , School of Life Sciences, , Shenzhen 518055, China"},{"name":"Department of Systems Biology , School of Life Sciences, , Shenzhen 518055, China"},{"name":"Southern University of Science and Technology , School of Life Sciences, , Shenzhen 518055, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yewen","family":"Xu","sequence":"additional","affiliation":[{"name":"Shenzhen Key Laboratory of Gene Regulation and Systems Biology , School of Life Sciences, , Shenzhen 518055, China"},{"name":"Southern University of Science and Technology , School of Life Sciences, , Shenzhen 518055, China"},{"name":"Department of Systems Biology , School of Life Sciences, , Shenzhen 518055, China"},{"name":"Southern University of Science and Technology , School of Life Sciences, , Shenzhen 518055, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yang","family":"Yang","sequence":"additional","affiliation":[{"name":"Shenzhen Key Laboratory of Gene Regulation and Systems Biology , School of Life Sciences, , Shenzhen 518055, China"},{"name":"Southern University of Science and Technology , School of Life Sciences, , Shenzhen 518055, China"},{"name":"Department of Systems Biology , School of Life Sciences, , Shenzhen 518055, China"},{"name":"Southern University of Science and Technology , School of Life Sciences, , Shenzhen 518055, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pengfei","family":"Yin","sequence":"additional","affiliation":[{"name":"Department of Systems Biology , School of Life Sciences, , Shenzhen 518055, China"},{"name":"Southern University of Science and Technology , School of Life Sciences, , Shenzhen 518055, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Duo","family":"Ning","sequence":"additional","affiliation":[{"name":"Shenzhen Key Laboratory of Gene Regulation and Systems Biology , School of Life Sciences, , Shenzhen 518055, China"},{"name":"Southern University of Science and Technology , School of Life Sciences, , Shenzhen 518055, China"},{"name":"Department of Systems Biology , School of Life Sciences, , Shenzhen 518055, China"},{"name":"Southern University of Science and Technology , School of Life Sciences, , Shenzhen 518055, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guangyu","family":"Huang","sequence":"additional","affiliation":[{"name":"Department of Systems Biology , School of Life Sciences, , Shenzhen 518055, China"},{"name":"Southern University of Science and Technology , School of Life Sciences, , Shenzhen 518055, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuqing","family":"Deng","sequence":"additional","affiliation":[{"name":"Department of Systems Biology , School of Life Sciences, , Shenzhen 518055, China"},{"name":"Southern University of Science and Technology , School of Life Sciences, , Shenzhen 518055, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gengzhan","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Systems Biology , School of Life Sciences, , Shenzhen 518055, China"},{"name":"Southern University of Science and Technology , School of Life Sciences, , Shenzhen 518055, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guoliang","family":"Li","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement , Hubei Hongshan Laboratory, , Wuhan 430070, China"},{"name":"Huazhong Agricultural University , Hubei Hongshan Laboratory, , Wuhan 430070, China"},{"name":"Agricultural Bioinformatics Key Laboratory of Hubei Province , Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, , Wuhan 430070, China"},{"name":"Huazhong Agricultural University , Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, , Wuhan 430070, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Simon Zhongyuan","family":"Tian","sequence":"additional","affiliation":[{"name":"Shenzhen Key Laboratory of Gene Regulation and Systems Biology , School of Life Sciences, , Shenzhen 518055, China"},{"name":"Southern University of Science and Technology , School of Life Sciences, , Shenzhen 518055, China"},{"name":"Department of Systems Biology , School of Life Sciences, , Shenzhen 518055, China"},{"name":"Southern University of Science and Technology , School of Life Sciences, , Shenzhen 518055, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Meizhen","family":"Zheng","sequence":"additional","affiliation":[{"name":"Shenzhen Key Laboratory of Gene Regulation and Systems Biology , School of Life Sciences, , Shenzhen 518055, China"},{"name":"Southern University of Science and Technology , School of Life Sciences, , Shenzhen 518055, China"},{"name":"Department of Systems Biology , School of Life Sciences, , Shenzhen 518055, China"},{"name":"Southern University of Science and Technology , School of Life Sciences, , Shenzhen 518055, 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