Revisiting the Briggs Ancient DNA Damage Model: A Fast Maximum Likelihood Method to Estimate Post-Mortem Damage.

ABSTRACT: One essential initial step in the analysis of ancient DNA is to authenticate that the DNA sequencing reads are actually from ancient DNA. This is done by assessing if the reads exhibit typical characteristics of post-mortem damage (PMD), including cytosine deamination and nicks. We present a novel statistical method implemented in a fast multithreaded programme, ngsBriggs that enables rapid quantification of PMD by estimation of the Briggs ancient damage model parameters (Briggs parameters). Using a multinomial model with maximum likelihood fit, ngsBriggs accurately estimates the parameters of the Briggs model, quantifying the PMD signal from single and double-stranded DNA regions. We extend the original Briggs model to capture PMD signals for contemporary sequencing platforms and show tha

SUBMITTER: Zhao L 

PROVIDER: S-EPMC11646307 | biostudies-literature | 2025 Jan

REPOSITORIES: biostudies-literature