mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters

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Standard

mapDamage2.0 : fast approximate Bayesian estimates of ancient DNA damage parameters. / Jónsson, Hákon; Ginolhac, Aurélien; Schubert, Mikkel; Johnson, Philip L. F.; Orlando, Ludovic Antoine Alexandre.

I: Bioinformatics, Bind 29, Nr. 13, 01.07.2013, s. 1682-1684.

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt

Harvard

Jónsson, H, Ginolhac, A, Schubert, M, Johnson, PLF & Orlando, LAA 2013, 'mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters', Bioinformatics, bind 29, nr. 13, s. 1682-1684. https://doi.org/10.1093/bioinformatics/btt193

APA

Jónsson, H., Ginolhac, A., Schubert, M., Johnson, P. L. F., & Orlando, L. A. A. (2013). mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics, 29(13), 1682-1684. https://doi.org/10.1093/bioinformatics/btt193

Vancouver

Jónsson H, Ginolhac A, Schubert M, Johnson PLF, Orlando LAA. mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics. 2013 jul. 1;29(13):1682-1684. https://doi.org/10.1093/bioinformatics/btt193

Author

Jónsson, Hákon ; Ginolhac, Aurélien ; Schubert, Mikkel ; Johnson, Philip L. F. ; Orlando, Ludovic Antoine Alexandre. / mapDamage2.0 : fast approximate Bayesian estimates of ancient DNA damage parameters. I: Bioinformatics. 2013 ; Bind 29, Nr. 13. s. 1682-1684.

Bibtex

@article{e7ae6add1d374014b137a39a75919590,
title = "mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters",
abstract = "Ancient DNA (aDNA) molecules in fossilized bones and teeth, coprolites, sediments, mummified specimens and museum collections represent fantastic sources of information for evolutionary biologists, revealing the agents of past epidemics and the dynamics of past populations. However, the analysis of aDNA generally faces two major issues. Firstly, sequences consist of a mixture of endogenous and various exogenous backgrounds, mostly microbial. Secondly, high nucleotide misincorporation rates can be observed as a result of severe post-mortem DNA damage. Such misincorporation patterns are instrumental to authenticate ancient sequences versus modern contaminants. We recently developed the user-friendly mapDamage package that identifies such patterns from next-generation sequencing (NGS) sequence datasets. The absence of formal statistical modeling of the DNA damage process, however, precluded rigorous quantitative comparisons across samples.",
author = "H{\'a}kon J{\'o}nsson and Aur{\'e}lien Ginolhac and Mikkel Schubert and Johnson, {Philip L. F.} and Orlando, {Ludovic Antoine Alexandre}",
year = "2013",
month = jul,
day = "1",
doi = "10.1093/bioinformatics/btt193",
language = "English",
volume = "29",
pages = "1682--1684",
journal = "Computer Applications in the Biosciences",
issn = "1471-2105",
publisher = "Oxford University Press",
number = "13",

}

RIS

TY - JOUR

T1 - mapDamage2.0

T2 - fast approximate Bayesian estimates of ancient DNA damage parameters

AU - Jónsson, Hákon

AU - Ginolhac, Aurélien

AU - Schubert, Mikkel

AU - Johnson, Philip L. F.

AU - Orlando, Ludovic Antoine Alexandre

PY - 2013/7/1

Y1 - 2013/7/1

N2 - Ancient DNA (aDNA) molecules in fossilized bones and teeth, coprolites, sediments, mummified specimens and museum collections represent fantastic sources of information for evolutionary biologists, revealing the agents of past epidemics and the dynamics of past populations. However, the analysis of aDNA generally faces two major issues. Firstly, sequences consist of a mixture of endogenous and various exogenous backgrounds, mostly microbial. Secondly, high nucleotide misincorporation rates can be observed as a result of severe post-mortem DNA damage. Such misincorporation patterns are instrumental to authenticate ancient sequences versus modern contaminants. We recently developed the user-friendly mapDamage package that identifies such patterns from next-generation sequencing (NGS) sequence datasets. The absence of formal statistical modeling of the DNA damage process, however, precluded rigorous quantitative comparisons across samples.

AB - Ancient DNA (aDNA) molecules in fossilized bones and teeth, coprolites, sediments, mummified specimens and museum collections represent fantastic sources of information for evolutionary biologists, revealing the agents of past epidemics and the dynamics of past populations. However, the analysis of aDNA generally faces two major issues. Firstly, sequences consist of a mixture of endogenous and various exogenous backgrounds, mostly microbial. Secondly, high nucleotide misincorporation rates can be observed as a result of severe post-mortem DNA damage. Such misincorporation patterns are instrumental to authenticate ancient sequences versus modern contaminants. We recently developed the user-friendly mapDamage package that identifies such patterns from next-generation sequencing (NGS) sequence datasets. The absence of formal statistical modeling of the DNA damage process, however, precluded rigorous quantitative comparisons across samples.

U2 - 10.1093/bioinformatics/btt193

DO - 10.1093/bioinformatics/btt193

M3 - Journal article

C2 - 23613487

VL - 29

SP - 1682

EP - 1684

JO - Computer Applications in the Biosciences

JF - Computer Applications in the Biosciences

SN - 1471-2105

IS - 13

ER -

ID: 48869841