AdDeam: A Fast and Scalable Tool for Estimating and Clustering Reference-Level Damage Profiles
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Motivation
DNA damage patterns, such as increased frequencies of C → T and G → A substitutions at fragment ends, are widely used in ancient DNA studies to assess authenticity and detect contamination. In metagenomic studies, fragments can be mapped against multiple references or de novo assembled contigs to identify those likely to be ancient. Generating and comparing damage profiles to identify samples or contigs that are likely to stem from modern contaminants, however, can be both tedious and time-consuming. Although tools exist for estimating damage in single reference genomes and metagenomic datasets, none efficiently cluster damage patterns.
Results
To address this methodological gap, we developed AdDeam, a tool that combines rapid damage estimation with clustering for streamlined analyses and easy identification of potential contaminants or outliers. Our tool takes aligned aDNA fragments from various samples or contigs as input, computes damage patterns, clusters them and outputs representative damage profiles per cluster, a probability of each sample of pertaining to a cluster as well as a PCA of the damage patterns for each sample for fast visualisation. We evaluated AdDeam on both simulated and empirical datasets. AdDeam effectively distinguishes different damage levels, such as UDG-treated samples, sample-specific damages from specimens of different time periods, and can also distinguish between contigs containing modern or ancient fragments, providing a clear framework for aDNA authentication and facilitating large-scale analyses. The software is publicly available at https://github.com/LouisPwr/AdDeam .
