title: mapDamage: testing for damage patterns in ancient DNA sequences.
abstract: CONCLUSIONS
  Ancient DNA extracts consist of a mixture of contaminant DNA molecules, most often originating from environmental microbes, and endogenous fragments exhibiting substantial levels of DNA damage. The latter introduce specific nucleotide misincorporations and DNA fragmentation signatures in sequencing reads that could be advantageously used to argue for sequence validity. mapDamage is a Perl script that computes nucleotide misincorporation and fragmentation patterns using next-generation sequencing reads mapped against a reference genome. The Perl script outputs are further automatically processed in embedded R script in order to detect typical patterns of genuine ancient DNA sequences.
  
  
  METHODS
  The Perl script mapDamage is freely available with documentation and example files at http://geogenetics.ku.dk/all_literature/mapdamage/. The script requires prior installation of the SAMtools suite and R environment and has been validated on both GNU/Linux and MacOSX operating systems.
authors.affiliation: Centre for Geogenetics, Natural History Museum of Denmark, Copenhagen University, 1350 København K, Denmark. aginolhac@snm.ku.dk
authors.forename: Aurelien
authors.initials: A
authors.lastname: Ginolhac
authors.forename: Morten
authors.initials: M
authors.lastname: Rasmussen
authors.forename: M Thomas P
authors.initials: MT
authors.lastname: Gilbert
authors.forename: Eske
authors.initials: E
authors.lastname: Willerslev
authors.forename: Ludovic
authors.initials: L
authors.lastname: Orlando
mesh_terms: D001483:Base Sequence; D019295:Computational Biology / Q000379:methods; D059018:DNA Contamination; D004249:DNA Damage / Q000235:genetics*; D004262:DNA Restriction Enzymes; D015894:Genome, Human; D006801:Humans; D010163:Paleontology; D012015:Reference Standards; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D004262:DNA Restriction Enzymes