mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters

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ID: 292108
2013
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Abstract
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.
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Authors Hákon Jónsson, Aurélien Ginolhac, Mikkel Schubert, Philip L. Johnson, Ludovic Orlando
Journal BMC Bioinformatics
Year 2013
DOI
10.1093/bioinformatics/btt193
URL
https://academic.oup.com/bioinformatics/article-pdf/29/13/1682/18534019/btt193.pdf
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