Reference : mapDamage: testing for damage patterns in ancient DNA sequences.
Scientific journals : Article
Life sciences : Biochemistry, biophysics & molecular biology
http://hdl.handle.net/10993/24787
mapDamage: testing for damage patterns in ancient DNA sequences.
English
Ginolhac, Aurélien [University of Copenhagen > Centre for Geogenetics]
Rasmussen, Morten [> >]
Gilbert, M. Thomas P. [> >]
Willerslev, Eske [> >]
Orlando, Ludovic [> >]
2011
Bioinformatics (Oxford, England)
27
15
2153-5
Yes (verified by ORBilu)
1367-4803
1367-4811
England
[en] Base Sequence ; Computational Biology/methods ; DNA Contamination ; DNA Damage/genetics ; DNA Restriction Enzymes ; Genome, Human ; Humans ; Paleontology ; Reference Standards ; Sequence Analysis, DNA/methods ; Software
[en] SUMMARY: 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.
http://hdl.handle.net/10993/24787

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