{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,10]],"date-time":"2026-04-10T23:04:54Z","timestamp":1775862294218,"version":"3.50.1"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2023,1,20]],"date-time":"2023-01-20T00:00:00Z","timestamp":1674172800000},"content-version":"vor","delay-in-days":19,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Lundbeck Foundation Centre for Disease Evolution","award":["R302-2018-2155"],"award-info":[{"award-number":["R302-2018-2155"]}]},{"name":"Carlsberg Foundation in 2019"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Summary<\/jats:title><jats:p>With the rapid expansion of the capabilities of the DNA sequencers throughout the different sequencing generations, the quantity of generated data has likewise increased. This evolution has also led to new bioinformatical methods, for which in silico data have become crucial when verifying the accuracy of a model or the robustness of a genomic analysis pipeline. Here, we present a multithreaded next-generation simulator for next-generation sequencing data (NGSNGS), which simulates reads faster than currently available methods and programs. NGSNGS can simulate reads with platform-specific characteristics based on nucleotide quality score profiles as well as including a post-mortem damage model which is relevant for simulating ancient DNA. The simulated sequences are sampled (with replacement) from a reference DNA genome, which can represent a haploid genome, polyploid assemblies or even population haplotypes and allows the user to simulate known variable sites directly. The program is implemented in a multithreading framework and is factors faster than currently available tools while extending their feature set and possible output formats.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>The method and associated programs are released as open-source software, code and user manual are available at https:\/\/github.com\/RAHenriksen\/NGSNGS.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad041","type":"journal-article","created":{"date-parts":[[2023,1,19]],"date-time":"2023-01-19T14:13:54Z","timestamp":1674137634000},"source":"Crossref","is-referenced-by-count":23,"title":["NGSNGS: next-generation simulator for next-generation sequencing data"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3657-1983","authenticated-orcid":false,"given":"Rasmus Amund","family":"Henriksen","sequence":"first","affiliation":[{"name":"Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen , 1350 Copenhagen K, Denmark"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6551-2707","authenticated-orcid":false,"given":"Lei","family":"Zhao","sequence":"additional","affiliation":[{"name":"Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen , 1350 Copenhagen K, Denmark"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7576-5380","authenticated-orcid":false,"given":"Thorfinn Sand","family":"Korneliussen","sequence":"additional","affiliation":[{"name":"Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen , 1350 Copenhagen K, Denmark"}]}],"member":"286","published-online":{"date-parts":[[2023,1,20]]},"reference":[{"key":"2023020115551842400_btad041-B1","doi-asserted-by":"crossref","first-page":"14616","DOI":"10.1073\/pnas.0704665104","article-title":"Patterns of damage in genomic DNA sequences from a Neandertal","volume":"104","author":"Briggs","year":"2007","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023020115551842400_btad041-B2","doi-asserted-by":"crossref","first-page":"a012567","DOI":"10.1101\/cshperspect.a012567","article-title":"Ancient DNA damage","volume":"5","author":"Dabney","year":"2013","journal-title":"Cold Spring Harbor Perspect. Biol"},{"key":"2023020115551842400_btad041-B3","doi-asserted-by":"crossref","first-page":"801","DOI":"10.1016\/j.humimm.2021.02.012","article-title":"Next-generation sequencing technologies: an overview","volume":"82","author":"Hu","year":"2021","journal-title":"Hum. Immunol"},{"key":"2023020115551842400_btad041-B4","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1093\/bioinformatics\/btr708","article-title":"Art: a next-generation sequencing read simulator","volume":"28","author":"Huang","year":"2012","journal-title":"Bioinformatics"},{"key":"2023020115551842400_btad041-B5","doi-asserted-by":"crossref","first-page":"1682","DOI":"10.1093\/bioinformatics\/btt193","article-title":"mapdamage2. 0: fast approximate Bayesian estimates of ancient DNA damage parameters","volume":"29","author":"J\u00f3nsson","year":"2013","journal-title":"Bioinformatics"},{"key":"2023020115551842400_btad041-B6","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s43586-020-00011-0","article-title":"Ancient DNA analysis","volume":"1","author":"Orlando","year":"2021","journal-title":"Nat. Rev. Methods Primers"},{"key":"2023020115551842400_btad041-B7","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/gb-2010-11-5-r47","article-title":"Computational challenges in the analysis of ancient DNA","volume":"11","author":"Pr\u00fcfer","year":"2010","journal-title":"Genome Biol"},{"key":"2023020115551842400_btad041-B8","doi-asserted-by":"crossref","first-page":"577","DOI":"10.1093\/bioinformatics\/btw670","article-title":"Gargammel: a sequence simulator for ancient DNA","volume":"33","author":"Renaud","year":"2017","journal-title":"Bioinformatics"},{"key":"2023020115551842400_btad041-B9","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1098\/rspb.2004.2813","article-title":"Ancient DNA","volume":"272","author":"Willerslev","year":"2005","journal-title":"Proc. R. Soc. B"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btad041\/48800233\/btad041.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/1\/btad041\/49030524\/btad041.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/1\/btad041\/49030524\/btad041.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,3,21]],"date-time":"2023-03-21T16:39:50Z","timestamp":1679416790000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btad041\/6994180"}},"subtitle":[],"editor":[{"given":"Can","family":"Alkan","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2023,1,1]]},"references-count":9,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2023,1,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btad041","relation":{},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,1,1]]},"published":{"date-parts":[[2023,1,1]]},"article-number":"btad041"}}