{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,2]],"date-time":"2026-09-02T03:41:20Z","timestamp":1788320480478,"version":"build-2803163510"},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2024,9,27]],"date-time":"2024-09-27T00:00:00Z","timestamp":1727395200000},"content-version":"vor","delay-in-days":4,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Heilongjiang Postdoctoral Foundation","award":["LBHZ22174"],"award-info":[{"award-number":["LBHZ22174"]}]},{"DOI":"10.13039\/501100002858","name":"China Postdoctoral Science Foundation","doi-asserted-by":"publisher","award":["2022\u00a0M720965"],"award-info":[{"award-number":["2022\u00a0M720965"]}],"id":[{"id":"10.13039\/501100002858","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62202125"],"award-info":[{"award-number":["62202125"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62172125"],"award-info":[{"award-number":["62172125"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2021YFF1200105"],"award-info":[{"award-number":["2021YFF1200105"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2022YFF1202101"],"award-info":[{"award-number":["2022YFF1202101"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,9,23]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Nanopore sequence technology has demonstrated a longer read length and enabled to potentially address the limitations of short-read sequencing including long-range haplotype phasing and accurate variant calling. However, there is still room for improvement in terms of the performance of single nucleotide variant (SNV) identification and computing resource usage for the state-of-the-art approaches. In this work, we introduce miniSNV, a lightweight SNV calling algorithm that simultaneously achieves high performance and yield. miniSNV utilizes known common variants in populations as variation backgrounds and leverages read pileup, read-based phasing, and consensus generation to identify and genotype SNVs for Oxford Nanopore Technologies (ONT) long reads. Benchmarks on real and simulated ONT data under various error profiles demonstrate that miniSNV has superior sensitivity and comparable accuracy on SNV detection and runs faster with outstanding scalability and lower memory than most state-of-the-art variant callers. miniSNV is available from https:\/\/github.com\/CuiMiao-HIT\/miniSNV.<\/jats:p>","DOI":"10.1093\/bib\/bbae473","type":"journal-article","created":{"date-parts":[[2024,9,27]],"date-time":"2024-09-27T13:06:04Z","timestamp":1727442364000},"source":"Crossref","is-referenced-by-count":9,"title":["miniSNV: accurate and fast single nucleotide variant calling from nanopore sequencing data"],"prefix":"10.1093","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0009-0002-1413-7887","authenticated-orcid":false,"given":"Miao","family":"Cui","sequence":"first","affiliation":[{"name":"Faculty of Computing, Harbin Institute of Technology , 92 Xidazhi Street, Nangang District, Harbin, Heilongjiang 150001,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yadong","family":"Liu","sequence":"additional","affiliation":[{"name":"Faculty of Computing, Harbin Institute of Technology , 92 Xidazhi Street, Nangang District, Harbin, Heilongjiang 150001,","place":["China"]},{"name":"Zhengzhou Research Institute, Harbin Institute of Technology , 26 Longyuan East 7th Street, Zhengdong New District, Zhengzhou, Henan 450000,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-1917-143X","authenticated-orcid":false,"given":"Xian","family":"Yu","sequence":"additional","affiliation":[{"name":"Faculty of Computing, Harbin Institute of Technology , 92 Xidazhi Street, Nangang District, Harbin, Heilongjiang 150001,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6201-6655","authenticated-orcid":false,"given":"Hongzhe","family":"Guo","sequence":"additional","affiliation":[{"name":"Faculty of Computing, Harbin Institute of Technology , 92 Xidazhi Street, Nangang District, Harbin, Heilongjiang 150001,","place":["China"]},{"name":"Zhengzhou Research Institute, Harbin Institute of Technology , 26 Longyuan East 7th Street, Zhengdong New District, Zhengzhou, Henan 450000,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0673-8503","authenticated-orcid":false,"given":"Tao","family":"Jiang","sequence":"additional","affiliation":[{"name":"Faculty of Computing, Harbin Institute of Technology , 92 Xidazhi Street, Nangang District, Harbin, Heilongjiang 150001,","place":["China"]},{"name":"Zhengzhou Research Institute, Harbin Institute of Technology , 26 Longyuan East 7th Street, Zhengdong New District, Zhengzhou, Henan 450000,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6500-6217","authenticated-orcid":false,"given":"Yadong","family":"Wang","sequence":"additional","affiliation":[{"name":"Faculty of Computing, Harbin Institute of Technology , 92 Xidazhi Street, Nangang District, Harbin, Heilongjiang 150001,","place":["China"]},{"name":"Zhengzhou Research Institute, Harbin Institute of Technology , 26 Longyuan East 7th Street, Zhengdong New District, Zhengzhou, Henan 450000,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bo","family":"Liu","sequence":"additional","affiliation":[{"name":"Faculty of Computing, Harbin Institute of Technology , 92 Xidazhi Street, Nangang District, Harbin, Heilongjiang 150001,","place":["China"]},{"name":"Zhengzhou Research Institute, Harbin Institute of Technology , 26 Longyuan East 7th Street, Zhengdong New District, Zhengzhou, Henan 450000,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,9,27]]},"reference":[{"key":"2024092713054899500_ref1","doi-asserted-by":"publisher","first-page":"0561","DOI":"10.1007\/s100380200086","article-title":"SNP alleles in human disease and evolution","volume":"47","author":"Shastry","year":"2002","journal-title":"J Hum Genet"},{"key":"2024092713054899500_ref2","doi-asserted-by":"publisher","first-page":"443","DOI":"10.1038\/nrg2986","article-title":"Genotype and SNP calling from next-generation sequencing data","volume":"12","author":"Nielsen","year":"2011","journal-title":"Nat Rev Genet"},{"key":"2024092713054899500_ref3","doi-asserted-by":"publisher","first-page":"345","DOI":"10.1038\/nature24286","article-title":"DNA sequencing at 40: past, present and future","volume":"550","author":"Shendure","year":"2017","journal-title":"Nature"},{"key":"2024092713054899500_ref4","doi-asserted-by":"publisher","first-page":"1869","DOI":"10.1038\/s41467-019-09637-5","article-title":"Sequencing of human genomes with nanopore technology","volume":"10","author":"Bowden","year":"2019","journal-title":"Nat Commun"},{"key":"2024092713054899500_ref5","doi-asserted-by":"publisher","first-page":"4660","DOI":"10.1038\/s41467-019-12493-y","article-title":"Longshot enables accurate variant calling in diploid genomes from single-molecule long read sequencing","volume":"10","author":"Edge","year":"2019","journal-title":"Nat Commun"},{"key":"2024092713054899500_ref6","doi-asserted-by":"publisher","first-page":"1322","DOI":"10.1038\/s41592-021-01299-w","article-title":"Haplotype-aware variant calling with PEPPER-margin-DeepVariant enables high accuracy in nanopore long-reads","volume":"18","author":"Shafin","year":"2021","journal-title":"Nat Methods"},{"key":"2024092713054899500_ref7","doi-asserted-by":"publisher","DOI":"10.3389\/fcell.2021.731424","article-title":"Psi-caller: a lightweight short read-based variant caller with high speed and accuracy","volume":"9","author":"Liu","year":"2021","journal-title":"Frontiers in Cell and Developmental Biology"},{"key":"2024092713054899500_ref8","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13059-016-1103-0","article-title":"The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community","volume":"17","author":"Jain","year":"2016","journal-title":"Genome Biol"},{"key":"2024092713054899500_ref9","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/gb-2013-14-6-405","article-title":"The advantages of SMRT sequencing","volume":"14","author":"Roberts","year":"2013","journal-title":"Genome Biol"},{"key":"2024092713054899500_ref10","doi-asserted-by":"publisher","first-page":"329","DOI":"10.1038\/s41576-018-0003-4","article-title":"Piercing the dark matter: bioinformatics of long-range sequencing and mapping","volume":"19","author":"Sedlazeck","year":"2018","journal-title":"Nat Rev Genet"},{"key":"2024092713054899500_ref11","doi-asserted-by":"publisher","first-page":"338","DOI":"10.1038\/nbt.4060","article-title":"Nanopore sequencing and assembly of a human genome with ultra-long reads","volume":"36","author":"Jain","year":"2018","journal-title":"Nat Biotechnol"},{"key":"2024092713054899500_ref12","doi-asserted-by":"publisher","first-page":"1044","DOI":"10.1038\/s41587-020-0503-6","article-title":"Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes","volume":"38","author":"Shafin","year":"2020","journal-title":"Nat Biotechnol"},{"key":"2024092713054899500_ref13","doi-asserted-by":"publisher","first-page":"1155","DOI":"10.1038\/s41587-019-0217-9","article-title":"Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome","volume":"37","author":"Wenger","year":"2019","journal-title":"Nat Biotechnol"},{"key":"2024092713054899500_ref14","doi-asserted-by":"publisher","first-page":"90","DOI":"10.1186\/s13059-018-1462-9","article-title":"From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy","volume":"19","author":"Rang","year":"2018","journal-title":"Genome Biol"},{"key":"2024092713054899500_ref15","author":"O. N. T. Dorado"},{"key":"2024092713054899500_ref16","author":"EPI2ME"},{"key":"2024092713054899500_ref17","doi-asserted-by":"publisher","first-page":"797","DOI":"10.1038\/s43588-022-00387-x","article-title":"Symphonizing pileup and full-alignment for deep learning-based long-read variant calling","volume":"2","author":"Zheng","year":"2022","journal-title":"Nature Computational Science"},{"key":"2024092713054899500_ref18","doi-asserted-by":"publisher","first-page":"220","DOI":"10.1038\/s42256-020-0167-4","article-title":"Exploring the limit of using a deep neural network on pileup data for germline variant calling","volume":"2","author":"Luo","year":"2020","journal-title":"Nature Machine Intelligence"},{"key":"2024092713054899500_ref19","doi-asserted-by":"publisher","first-page":"983","DOI":"10.1038\/nbt.4235","article-title":"A universal SNP and small-indel variant caller using deep neural networks","volume":"36","author":"Poplin","year":"2018","journal-title":"Nat Biotechnol"},{"key":"2024092713054899500_ref20","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13059-021-02472-2","article-title":"NanoCaller for accurate detection of SNPs and indels in difficult-to-map regions from long-read sequencing by haplotype-aware deep neural networks","volume":"22","author":"Ahsan","year":"2021","journal-title":"Genome Biol"},{"key":"2024092713054899500_ref21","doi-asserted-by":"publisher","first-page":"1784","DOI":"10.1038\/s41467-018-08148-z","article-title":"Multi-platform discovery of haplotype-resolved structural variation in human genomes","volume":"10","author":"Chaisson","year":"2019","journal-title":"Nat Commun"},{"key":"2024092713054899500_ref22","doi-asserted-by":"publisher","first-page":"1050","DOI":"10.1038\/nmeth.4035","article-title":"Phased diploid genome assembly with single-molecule real-time sequencing","volume":"13","author":"Chin","year":"2016","journal-title":"Nat Methods"},{"key":"2024092713054899500_ref23","doi-asserted-by":"publisher","first-page":"801","DOI":"10.1101\/gr.213462.116","article-title":"HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies","volume":"27","author":"Edge","year":"2017","journal-title":"Genome Res"},{"key":"2024092713054899500_ref24","doi-asserted-by":"publisher","first-page":"677","DOI":"10.1101\/gr.214007.116","article-title":"Discovery and genotyping of structural variation from long-read haploid genome sequence data","volume":"27","author":"Huddleston","year":"2017","journal-title":"Genome Res"},{"key":"2024092713054899500_ref25"},{"key":"2024092713054899500_ref26","doi-asserted-by":"publisher","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":"2024092713054899500_ref27","doi-asserted-by":"publisher","first-page":"498","DOI":"10.1089\/cmb.2014.0157","article-title":"WhatsHap: weighted haplotype assembly for future-generation sequencing reads","volume":"22","author":"Patterson","year":"2015","journal-title":"J Comput Biol"},{"key":"2024092713054899500_ref28","doi-asserted-by":"publisher","first-page":"2209","DOI":"10.1093\/bioinformatics\/btaa963","article-title":"abPOA: an SIMD-based C library for fast partial order alignment using adaptive band","volume":"37","author":"Gao","year":"2021","journal-title":"Bioinformatics"},{"key":"2024092713054899500_ref29","doi-asserted-by":"crossref","first-page":"btae014","DOI":"10.1093\/bioinformatics\/btae014","article-title":"FMAlign2: a novel fast multiple nucleotide sequence alignment method for ultralong datasets","volume":"40","author":"Zhang","year":"2024","journal-title":"Bioinformatics"},{"key":"2024092713054899500_ref30","doi-asserted-by":"publisher","first-page":"msac166","DOI":"10.1093\/molbev\/msac166","article-title":"HAlign 3: fast multiple alignment of ultra-large numbers of similar DNA\/RNA sequences","volume":"39","author":"Tang","year":"2022","journal-title":"Mol Biol Evol"},{"key":"2024092713054899500_ref31","doi-asserted-by":"publisher","first-page":"1220","DOI":"10.1093\/bioinformatics\/btv710","article-title":"Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications","volume":"32","author":"Chen","year":"2016","journal-title":"Bioinformatics"},{"key":"2024092713054899500_ref32","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1186\/s12859-018-2014-8","article-title":"Introducing difference recurrence relations for faster semi-global alignment of long sequences","volume":"19","author":"Suzuki","year":"2018","journal-title":"BMC bioinformatics"},{"key":"2024092713054899500_ref33","doi-asserted-by":"publisher","first-page":"196197","DOI":"10.1109\/ACCESS.2020.3034343","article-title":"Transfer learning with adaptive fine-tuning","volume":"8","author":"Vrban\u010di\u010d","year":"2020","journal-title":"IEEE Access"},{"key":"2024092713054899500_ref34","doi-asserted-by":"publisher","first-page":"1483","DOI":"10.1038\/s41592-023-01993-x","article-title":"Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation","volume":"20","author":"Kolmogorov","year":"2023","journal-title":"Nat Methods"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/25\/6\/bbae473\/59368743\/bbae473.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/25\/6\/bbae473\/59368743\/bbae473.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,9,27]],"date-time":"2024-09-27T13:06:08Z","timestamp":1727442368000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbae473\/7779241"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,9,23]]},"references-count":34,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2024,9,23]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbae473","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2024,11]]},"published":{"date-parts":[[2024,9,23]]},"article-number":"bbae473"}}