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

Abstract

7Summary 8 Contamination from present-day DNA is a fundamental issue when studying ancient DNA from 9 historical or archaeological material, and quantifying the amount of contamination is essential for 10 downstream analyses. We present AuthentiCT, a command-line tool to estimate the proportion of 11 present-day DNA contamination in ancient DNA datasets generated from single-stranded DNA 12 libraries. The prediction is based solely on the patterns of post-mortem damage observed on ancient 13 DNA sequences. The method has the power to quantify contamination from as few as 10,000 mapped 14 sequences, making it particularly useful for analysing specimens that are poorly preserved or for which

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

“…An open-source implementation of AuthentiCT in python and a test dataset are available on GitHub https://github. com/StephanePeyregne/AuthentiCT, under the GPLv3 [69]. The version of the source code used in this manuscript has also been deposited in Zenodo and referenced as https://doi.org/10.5281/zenodo.3948256 [70].…”

Present‐Day DNA Contamination in Ancient DNA Datasets

“…By taking into account the dependence between C‐to‐T substitutions along ancient DNA sequences, a more recent method models the observed frequency of damage‐associated substitutions in single‐ and double‐stranded parts of the original DNA fragments. [ 85 ] Each sequence originates from either contamination, which does not contain damage, or an ancient molecule that contains damage according to the explicit model of the structure of ancient DNA fragments. Like the previous method, the approach estimates contamination as the mixture proportion of sequences fitting to one of these two models.…”