mapDamage: testing for damage patterns in ancient DNA sequences

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

mapDamage : testing for damage patterns in ancient DNA sequences. / Ginolhac, Aurélien; Rasmussen, Morten; Gilbert, Tom; Willerslev, Eske; Orlando, Ludovic Antoine Alexandre.

In: Bioinformatics, Vol. 27, No. 15, 01.08.2011, p. 2153-2155.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Ginolhac, A, Rasmussen, M, Gilbert, T, Willerslev, E & Orlando, LAA 2011, 'mapDamage: testing for damage patterns in ancient DNA sequences', Bioinformatics, vol. 27, no. 15, pp. 2153-2155. https://doi.org/10.1093/bioinformatics/btr347

APA

Ginolhac, A., Rasmussen, M., Gilbert, T., Willerslev, E., & Orlando, L. A. A. (2011). mapDamage: testing for damage patterns in ancient DNA sequences. Bioinformatics, 27(15), 2153-2155. https://doi.org/10.1093/bioinformatics/btr347

Vancouver

Ginolhac A, Rasmussen M, Gilbert T, Willerslev E, Orlando LAA. mapDamage: testing for damage patterns in ancient DNA sequences. Bioinformatics. 2011 Aug 1;27(15):2153-2155. https://doi.org/10.1093/bioinformatics/btr347

Author

Ginolhac, Aurélien ; Rasmussen, Morten ; Gilbert, Tom ; Willerslev, Eske ; Orlando, Ludovic Antoine Alexandre. / mapDamage : testing for damage patterns in ancient DNA sequences. In: Bioinformatics. 2011 ; Vol. 27, No. 15. pp. 2153-2155.

Bibtex

@article{316ec411e7b64c579cf2d069f5412b95,
title = "mapDamage: testing for damage patterns in ancient DNA sequences",
abstract = "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 https://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.",
author = "Aur{\'e}lien Ginolhac and Morten Rasmussen and Tom Gilbert and Eske Willerslev and Orlando, {Ludovic Antoine Alexandre}",
year = "2011",
month = aug,
day = "1",
doi = "10.1093/bioinformatics/btr347",
language = "English",
volume = "27",
pages = "2153--2155",
journal = "Computer Applications in the Biosciences",
issn = "1471-2105",
publisher = "Oxford University Press",
number = "15",

}

RIS

TY - JOUR

T1 - mapDamage

T2 - testing for damage patterns in ancient DNA sequences

AU - Ginolhac, Aurélien

AU - Rasmussen, Morten

AU - Gilbert, Tom

AU - Willerslev, Eske

AU - Orlando, Ludovic Antoine Alexandre

PY - 2011/8/1

Y1 - 2011/8/1

N2 - 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 https://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.

AB - 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 https://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.

U2 - 10.1093/bioinformatics/btr347

DO - 10.1093/bioinformatics/btr347

M3 - Journal article

C2 - 21659319

VL - 27

SP - 2153

EP - 2155

JO - Computer Applications in the Biosciences

JF - Computer Applications in the Biosciences

SN - 1471-2105

IS - 15

ER -

ID: 33910533