{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,10]],"date-time":"2026-07-10T16:45:37Z","timestamp":1783701937004,"version":"3.55.0"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2016,12,6]],"date-time":"2016-12-06T00:00:00Z","timestamp":1480982400000},"content-version":"vor","delay-in-days":15,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Danish Council for Independent Research, Natural Sciences","award":["4002-00152B"],"award-info":[{"award-number":["4002-00152B"]}]},{"DOI":"10.13039\/501100001732","name":"Danish National Research Foundation","doi-asserted-by":"crossref","award":["DNRF94"],"award-info":[{"award-number":["DNRF94"]}],"id":[{"id":"10.13039\/501100001732","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100008398","name":"Villum Fonden","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100008398","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Initiative d\u2019Excellence Chaires d\u2019attractivit\u00e9, Universit\u00e9 de Toulouse"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Ancient DNA has emerged as a remarkable tool to infer the history of extinct species and past populations. However, many of its characteristics, such as extensive fragmentation, damage and contamination, can influence downstream analyses. To help investigators measure how these could impact their analyses in silico, we have developed gargammel, a package that simulates ancient DNA fragments given a set of known reference genomes. Our package simulates the entire molecular process from post-mortem DNA fragmentation and DNA damage to experimental sequencing errors, and reproduces most common bias observed in ancient DNA datasets.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>The package is publicly available on github: https:\/\/grenaud.github.io\/gargammel\/ and released under the GPL.<\/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\/btw670","type":"journal-article","created":{"date-parts":[[2016,10,21]],"date-time":"2016-10-21T19:05:23Z","timestamp":1477076723000},"page":"577-579","source":"Crossref","is-referenced-by-count":138,"title":["gargammel: a sequence simulator for ancient DNA"],"prefix":"10.1093","volume":"33","author":[{"given":"Gabriel","family":"Renaud","sequence":"first","affiliation":[{"name":"Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kristian","family":"Hangh\u00f8j","sequence":"additional","affiliation":[{"name":"Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark"},{"name":"Universit\u00e9 de Toulouse, University Paul Sabatier (UPS), Laboratoire AMIS, CNRS UMR, Toulouse, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eske","family":"Willerslev","sequence":"additional","affiliation":[{"name":"Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark"},{"name":"Department of Zoology, University of Cambridge, Cambridge, UK"},{"name":"Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ludovic","family":"Orlando","sequence":"additional","affiliation":[{"name":"Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark"},{"name":"Universit\u00e9 de Toulouse, University Paul Sabatier (UPS), Laboratoire AMIS, CNRS UMR, Toulouse, France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2016,11,21]]},"reference":[{"key":"2023020204422671800_btw670-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. 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Evol"},{"key":"2023020204422671800_btw670-B3","doi-asserted-by":"crossref","first-page":"2494","DOI":"10.1038\/emboj.2009.222","article-title":"The Neandertal genome and ancient DNA authenticity","volume":"28","author":"Green","year":"2009","journal-title":"EMBO J"},{"key":"2023020204422671800_btw670-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":"2023020204422671800_btw670-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":"2023020204422671800_btw670-B6","doi-asserted-by":"crossref","first-page":"syw059.","DOI":"10.1093\/sysbio\/syw059","article-title":"Evolutionary patterns and processes: lessons from ancient DNA","author":"Leonardi","year":"2016","journal-title":"Syst. 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