Bamdam: a post-mapping authentication toolkit for ancient metagenomics

Abstract

Ancient metagenomic studies using capture or shotgun sequencing often perform pairwise alignment of individual reads against large reference databases followed by lowest common ancestor assignment for taxonomic identification. Here, we present bamdam, a lightweight post-mapping, post lowest common ancestor toolkit for eukaryotic or microbial metagenomics. Bamdam can shrink large metagenomics bam files, often by a factor of 10x or more, while retaining all informative reads and alignments, compute a suite of authentication metrics for each taxonomic node including k-mer duplicity, postmortem damage, and mean read complexity, and generate various visualizations including multi-sample deamination plots and damage-colored interactive Krona plots. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-025-03879-x. Keywords: Metagenomics, Environmental DNA, Ancient DNA, Read complexity, Authentication