{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,4]],"date-time":"2026-08-04T09:55:36Z","timestamp":1785837336258,"version":"3.56.0"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"13","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1258,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Ancient DNA (aDNA) molecules in fossilized bones and teeth, coprolites, sediments, mummified specimens and museum collections represent fantastic sources of information for evolutionary biologists, revealing the agents of past epidemics and the dynamics of past populations. However, the analysis of aDNA generally faces two major issues. Firstly, sequences consist of a mixture of endogenous and various exogenous backgrounds, mostly microbial. Secondly, high nucleotide misincorporation rates can be observed as a result of severe post-mortem DNA damage. Such misincorporation patterns are instrumental to authenticate ancient sequences versus modern contaminants. We recently developed the user-friendly mapDamage package that identifies such patterns from next-generation sequencing (NGS) sequence datasets. The absence of formal statistical modeling of the DNA damage process, however, precluded rigorous quantitative comparisons across samples.<\/jats:p>\n               <jats:p>Results: Here, we describe mapDamage 2.0 that extends the original features of mapDamage by incorporating a statistical model of DNA damage. Assuming that damage events depend only on sequencing position and post-mortem deamination, our Bayesian statistical framework provides estimates of four key features of aDNA molecules: the average length of overhangs (\u03bb), nick frequency (\u03bd) and cytosine deamination rates in both double-stranded regions () and overhangs (). Our model enables rescaling base quality scores according to their probability of being damaged. mapDamage 2.0 handles NGS datasets with ease and is compatible with a wide range of DNA library protocols.<\/jats:p>\n               <jats:p>Availability: mapDamage 2.0 is available at ginolhac.github.io\/mapDamage\/ as a Python package and documentation is maintained at the Centre for GeoGenetics Web site (geogenetics.ku.dk\/publications\/mapdamage2.0\/).<\/jats:p>\n               <jats:p>Contact: \u00a0jonsson.hakon@gmail.com<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt193","type":"journal-article","created":{"date-parts":[[2013,4,24]],"date-time":"2013-04-24T03:35:45Z","timestamp":1366774545000},"page":"1682-1684","source":"Crossref","is-referenced-by-count":1635,"title":["mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters"],"prefix":"10.1093","volume":"29","author":[{"given":"H\u00e1kon","family":"J\u00f3nsson","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aur\u00e9lien","family":"Ginolhac","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mikkel","family":"Schubert","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philip L. F.","family":"Johnson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ludovic","family":"Orlando","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2013,4,23]]},"reference":[{"key":"2023062614231071600_btt193-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":"2023062614231071600_btt193-B2","doi-asserted-by":"crossref","first-page":"2153","DOI":"10.1093\/bioinformatics\/btr347","article-title":"mapDamage: testing for damage patterns in ancient DNA sequences","volume":"27","author":"Ginolhac","year":"2011","journal-title":"Bioinformatics"},{"key":"2023062614231071600_btt193-B3","doi-asserted-by":"crossref","first-page":"160","DOI":"10.1007\/BF02101694","article-title":"Dating of the human-ape splitting by a molecular clock of mitochondrial DNA","volume":"22","author":"Hasegawa","year":"1985","journal-title":"J. Mol. 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Protoc."},{"key":"2023062614231071600_btt193-B6","doi-asserted-by":"crossref","first-page":"222","DOI":"10.1126\/science.1224344","article-title":"A high-coverage genome sequence from an archaic denisovan individual","volume":"338","author":"Meyer","year":"2012","journal-title":"Science"},{"key":"2023062614231071600_btt193-B7","doi-asserted-by":"crossref","first-page":"645","DOI":"10.1146\/annurev.genet.37.110801.143214","article-title":"Genetic analyses from ancient DNA","volume":"38","author":"P\u00e4\u00e4bo","year":"2004","journal-title":"Annu. Rev. Genet."},{"key":"2023062614231071600_btt193-B8","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1126\/science.1211177","article-title":"An aboriginal Australian genome reveals separate human dispersals into Asia","volume":"334","author":"Rasmussen","year":"2011","journal-title":"Science"},{"key":"2023062614231071600_btt193-B9","doi-asserted-by":"crossref","first-page":"e34131","DOI":"10.1371\/journal.pone.0034131","article-title":"Temporal patterns of nucleotide misincorporations and DNA fragmentation in ancient DNA","volume":"7","author":"Sawyer","year":"2012","journal-title":"PloS One"},{"key":"2023062614231071600_btt193-B10","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1186\/1471-2164-13-178","article-title":"Improving ancient DNA read mapping against modern reference genomes","volume":"13","author":"Schubert","year":"2012","journal-title":"BMC Genomics"},{"key":"2023062614231071600_btt193-B11","doi-asserted-by":"crossref","first-page":"E746","DOI":"10.1073\/pnas.1105107108","article-title":"Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid of Yersinia pestis from victims of the Black Death","volume":"108","author":"Schuenemann","year":"2011","journal-title":"Proc. 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