The paper introduces mapDamage 2.0, an advanced tool for estimating ancient DNA (aDNA) damage parameters from next-generation sequencing (NGS) datasets. The tool addresses two major issues in aDNA analysis: the mixture of endogenous and exogenous sequences and high nucleotide misincorporation rates due to post-mortem DNA damage. The Bayesian statistical framework in mapDamage 2.0 provides estimates of key features such as the average length of overhangs, nick frequency, and cytosine deamination rates. It also enables the rescaling of base quality scores based on the probability of damage, reducing noise in downstream SNP calling. The method is compatible with various DNA library protocols and has been validated on a range of aDNA datasets, demonstrating its effectiveness in authenticating ancient sequences and improving the quality of sequence data.The paper introduces mapDamage 2.0, an advanced tool for estimating ancient DNA (aDNA) damage parameters from next-generation sequencing (NGS) datasets. The tool addresses two major issues in aDNA analysis: the mixture of endogenous and exogenous sequences and high nucleotide misincorporation rates due to post-mortem DNA damage. The Bayesian statistical framework in mapDamage 2.0 provides estimates of key features such as the average length of overhangs, nick frequency, and cytosine deamination rates. It also enables the rescaling of base quality scores based on the probability of damage, reducing noise in downstream SNP calling. The method is compatible with various DNA library protocols and has been validated on a range of aDNA datasets, demonstrating its effectiveness in authenticating ancient sequences and improving the quality of sequence data.