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mapDamage: testing for damage patterns in ancient DNA sequences

Ginolhac, Aurelien ; Rasmussen, Morten ; Gilbert, M. Thomas P ; Willerslev, Eske ; Orlando, Ludovic

Bioinformatics, 2011-08, Vol.27 (15), p.2153-2155 [Periódico revisado por pares]

Oxford: Oxford University Press

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Título:
mapDamage: testing for damage patterns in ancient DNA sequences
Autor: Ginolhac, Aurelien ; Rasmussen, Morten ; Gilbert, M. Thomas P ; Willerslev, Eske ; Orlando, Ludovic
Assuntos: Base Sequence ; Biological and medical sciences ; Computational Biology - methods ; DNA Contamination ; DNA Damage - genetics ; DNA Restriction Enzymes ; Fundamental and applied biological sciences. Psychology ; General aspects ; Genome, Human ; Humans ; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects) ; Paleontology ; Reference Standards ; Sequence Analysis, DNA - methods ; Software
É parte de: Bioinformatics, 2011-08, Vol.27 (15), p.2153-2155
Notas: ObjectType-Article-1
SourceType-Scholarly Journals-1
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Descrição: 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. Contact: aginolhac@snm.ku.dk Supplementary information: Supplementary data available at Bioinformatics online
Editor: Oxford: Oxford University Press
Idioma: Inglês

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mapDamage: testing for damage patterns in ancient DNA sequences

Ginolhac, Aurelien ; Rasmussen, Morten ; Gilbert, M. Thomas P ; Willerslev, Eske ; Orlando, Ludovic

Oxford: Oxford University Press

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