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

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Dokumenter

  • Hákon Jónsson
  • Aurélien Ginolhac
  • Mikkel Schubert
  • Philip L. F. Johnson
  • Ludovic Antoine Alexandre Orlando
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.
OriginalsprogEngelsk
TidsskriftBioinformatics
Vol/bind29
Udgave nummer13
Sider (fra-til)1682-1684
Antal sider3
ISSN1367-4803
DOI
StatusUdgivet - 1 jul. 2013

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