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AuthentiCT: A model of ancient DNA damage to estimate the proportion of present-day DNA contamination

MPS-Authors
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Peyrégne,  Stéphane
Genomes, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

/persons/resource/persons212905

Peter,  Benjamin M.
Genetic Diversity through Space and Time, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

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Peyrégne_AuthentiCT_GenBiol_2020.pdf
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Supplementary Material (public)

Peyrégne_AuthentiCT_GenBiol_2020 _Suppl.1.docx
(Supplementary material), 3MB

Peyrégne_AuthentiCT_GenBiol_2020 _Suppl.2.gz
(Supplementary material), 13MB

Peyrégne_AuthentiCT_GenBiol_2020 _Suppl.3.docx
(Supplementary material), 18KB

Citation

Peyrégne, S., & Peter, B. M. (2020). AuthentiCT: A model of ancient DNA damage to estimate the proportion of present-day DNA contamination. Genome Biology, 21: 246. doi:10.1186/s13059-020-02123-y.


Cite as: http://hdl.handle.net/21.11116/0000-0007-0542-9
Abstract
Contamination from present-day DNA is a fundamental issue when studying ancient DNA from historical or archaeological material, and quantifying the amount of contamination is essential for downstream analyses. We present AuthentiCT, a command-line tool to estimate the proportion of present-day DNA contamination in ancient DNA datasets generated from single-stranded DNA libraries. The prediction is based solely on the patterns of post-mortem damage observed on ancient DNA sequences. The method has the power to quantify contamination from as few as 10,000 mapped sequences, making it particularly useful for analysing specimens that are poorly preserved or for which little data is available.