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<p>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 <i>k</i>-mer duplicity, postmortem damage, and mean read complexity, and generate various visualizations including multi-sample deamination plots and damage-colored interactive Krona plots.</p>

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Bamdam: a post-mapping authentication toolkit for ancient metagenomics

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2025年12月5日

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  • Bianca De Sanctis,
  • Cade Mirchandani,
  • Haoran Dong,
  • Ruairidh Macleod,
  • Russell Corbett-Detig,
  • Yucheng Wang

摘要

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.