Revisiting the Briggs ancient DNA damage model: a fast regression method to estimate postmortem damage

Abstract

MotivationOne essential initial step in the analysis of ancient DNA is to authenticate its ancientness to ensure reliable conclusions. That is, meticulously assessing whether next-generation sequencing reads exhibit ancient characteristics, with a particular focus on the postmortem damage (PMD) signal induced by cytosine deamination in the fragments termini. We present a novel statistical method implementation in a fast multithreaded program ngsBriggs that enables the rapid quantification of PMD by calculation of the Briggs ancient damage model parameters (Briggs parameters). ResultsUsing a fast multinomial regression approach, ngsBriggs accurately models the Briggs parameters, quantifying the PMD signal from single and double-stranded DNA regions. We revisit and extend the original Briggs model, with ngsBriggs modeling PMD signals for contemporary sequencing platforms. Furthermore, ngsBriggs asserts itself as a reliable and consistent tool, by accurately estimating the Briggs parameters across a variety of contamination levels. The classification accuracy of ngsBriggs significantly exceeds the current tool available when discerning ancient-from modern sequencing reads to decontaminate samples. Our novel method and implementation ngsBriggs outperforms existing tools regarding computational speed and accuracy, establishing its practicality and usability. Our tool, ngsBriggs offers a practical and accurate toolset for researchers seeking to authenticate ancient DNA and improve the quality of their data. Availabilityhttps://github.com/lz398/metadamage_briggs