mapDamage: testing for damage patterns in ancient DNA sequences

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningfagfællebedømt

Aurélien Ginolhac, Morten Rasmussen, Tom Gilbert, Eske Willerslev, Ludovic Antoine Alexandre Orlando

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. Availability and implementation: 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.
OriginalsprogEngelsk
TidsskriftBioinformatics
Vol/bind27
Udgave nummer15
Sider (fra-til)2153-2155
Antal sider3
ISSN1367-4803
DOI
StatusUdgivet - 1 aug. 2011

ID: 33910533