{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,1]],"date-time":"2026-04-01T11:07:48Z","timestamp":1775041668938,"version":"3.50.1"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"21","license":[{"start":{"date-parts":[[2019,5,22]],"date-time":"2019-05-22T00:00:00Z","timestamp":1558483200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"publisher","award":["ANR-16-CE12-0019"],"award-info":[{"award-number":["ANR-16-CE12-0019"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"publisher","award":["ANR-16-JPEC-0005"],"award-info":[{"award-number":["ANR-16-JPEC-0005"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"publisher","award":["ANR-15-IDEX-01"],"award-info":[{"award-number":["ANR-15-IDEX-01"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004097","name":"Fondation ARC pour la Recherche sur le Cancer","doi-asserted-by":"publisher","award":["PDF20150602803"],"award-info":[{"award-number":["PDF20150602803"]}],"id":[{"id":"10.13039\/501100004097","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Extreme Science and Engineering Discovery Environment","award":["TG-BIO170065"],"award-info":[{"award-number":["TG-BIO170065"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Simulated genomes with pre-defined and random genomic variants can be very useful for benchmarking genomic and bioinformatics analyses. Here we introduce simuG, a lightweight tool for simulating the full-spectrum of genomic variants (single nucleotide polymorphisms, Insertions\/Deletions, copy number variants, inversions and translocations) for any organisms (including human). The simplicity and versatility of simuG make it a unique general-purpose genome simulator for a wide-range of simulation-based applications.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Code in Perl along with user manual and testing data is available at https:\/\/github.com\/yjx1217\/simuG. This software is free for use under the MIT license.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz424","type":"journal-article","created":{"date-parts":[[2019,5,18]],"date-time":"2019-05-18T07:09:07Z","timestamp":1558163347000},"page":"4442-4444","source":"Crossref","is-referenced-by-count":59,"title":["simuG: a general-purpose genome simulator"],"prefix":"10.1093","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2122-9221","authenticated-orcid":false,"given":"Jia-Xing","family":"Yue","sequence":"first","affiliation":[{"name":"Universit\u00e9 C\u00f4te d'Azur , CNRS, INSERM, IRCAN, Nice 06107, France"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2318-0775","authenticated-orcid":false,"given":"Gianni","family":"Liti","sequence":"additional","affiliation":[{"name":"Universit\u00e9 C\u00f4te d'Azur , CNRS, INSERM, IRCAN, Nice 06107, France"}]}],"member":"286","published-online":{"date-parts":[[2019,5,22]]},"reference":[{"key":"2023062712493204000_btz424-B1","doi-asserted-by":"crossref","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":"2023062712493204000_btz424-B2","first-page":"9","article-title":"Haplotype-based variant detection from short-read sequencing","volume":"3907","author":"Garrison","year":"2012","journal-title":"arXiv1207"},{"key":"2023062712493204000_btz424-B3","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1093\/bioinformatics\/btr708","article-title":"ART: a next-generation sequencing read simulator","volume":"15","author":"Huang","year":"2012","journal-title":"Bioinformatics"},{"key":"2023062712493204000_btz424-B4","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":"2023062712493204000_btz424-B5","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2023062712493204000_btz424-B6","doi-asserted-by":"crossref","first-page":"2899","DOI":"10.1093\/bioinformatics\/bty223","article-title":"DeepSimulator: a deep simulator for Nanopore sequencing","volume":"34","author":"Li","year":"2018","journal-title":"Bioinformatics"},{"key":"2023062712493204000_btz424-B7","doi-asserted-by":"crossref","first-page":"1469","DOI":"10.1093\/bioinformatics\/btu828","article-title":"VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications","volume":"31","author":"Mu","year":"2015","journal-title":"Bioinformatics"},{"key":"2023062712493204000_btz424-B8","doi-asserted-by":"crossref","first-page":"40.","DOI":"10.1186\/1471-2105-15-40","article-title":"SInC: an accurate and fast error-model based simulator for SNPs, Indels and CNVs coupled with a read generator for short-read sequence data","volume":"15","author":"Pattnaik","year":"2014","journal-title":"BMC Bioinformatics"},{"key":"2023062712493204000_btz424-B9","article-title":"Scaling accurate genetic variant discovery to tens of thousands of samples","author":"Poplin","year":"2018","journal-title":"bioRxiv"},{"key":"2023062712493204000_btz424-B10","doi-asserted-by":"crossref","first-page":"1876","DOI":"10.1093\/bioinformatics\/btx091","article-title":"Simulome: a genome sequence and variant simulator","volume":"33","author":"Price","year":"2017","journal-title":"Bioinformatics"},{"key":"2023062712493204000_btz424-B11","doi-asserted-by":"crossref","first-page":"i333","DOI":"10.1093\/bioinformatics\/bts378","article-title":"DELLY: structural variant discovery by integrated paired-end and split-read analysis","volume":"28","author":"Rausch","year":"2012","journal-title":"Bioinformatics"},{"key":"2023062712493204000_btz424-B12","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1038\/s41592-018-0001-7","article-title":"Accurate detection of complex structural variations using single-molecule sequencing","volume":"15","author":"Sedlazeck","year":"2018","journal-title":"Nat. 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