title: mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters.
abstract: BACKGROUND
  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.
  
  
  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 (λ), nick frequency (ν) 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.
  
  
  BACKGROUND
  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/).
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 København K, Denmark. jonsson.hakon@gmail.com
authors.forename: Hákon
authors.initials: H
authors.lastname: Jónsson
authors.forename: Aurélien
authors.initials: A
authors.lastname: Ginolhac
authors.forename: Mikkel
authors.initials: M
authors.lastname: Schubert
authors.forename: Philip L F
authors.initials: PL
authors.lastname: Johnson
authors.forename: Ludovic
authors.initials: L
authors.lastname: Orlando
mesh_terms: D001499:Bayes Theorem; D003596:Cytosine / Q000378:metabolism; D004249:DNA Damage; D003641:Deamination; D005580:Fossils; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D017422:Sequence Analysis, DNA; D012984:Software
chemical_list: D003596:Cytosine