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<p>De novo assembly of ancient metagenomic datasets is a challenging task. Ultra-short fragment size and characteristic postmortem damage patterns of sequenced ancient DNA molecules leave current tools ill-equipped for ideal assembly. We present <Emphasis FontCategory="NonProportional">CarpeDeam</Emphasis>, a novel damage-aware de novo assembler designed specifically for ancient metagenomic samples. Utilizing maximum-likelihood frameworks that integrate sample-specific damage patterns, <Emphasis FontCategory="NonProportional">CarpeDeam</Emphasis> demonstrates improved recovery of longer continuous sequences and protein sequences in many simulated and empirical datasets compared to existing assemblers. As a pioneering ancient metagenome assembler, <Emphasis FontCategory="NonProportional">CarpeDeam</Emphasis> opens the door for new opportunities in functional and taxonomic analyses of ancient microbial communities.</p>

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CarpeDeam: a de novo metagenome assembler for heavily damaged ancient datasets

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2025年10月27日

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  • Louis Kraft,
  • Johannes Söding,
  • Martin Steinegger,
  • Annika Jochheim,
  • Peter Wad Sackett,
  • Antonio Fernandez-Guerra,
  • Gabriel Renaud

摘要

De novo assembly of ancient metagenomic datasets is a challenging task. Ultra-short fragment size and characteristic postmortem damage patterns of sequenced ancient DNA molecules leave current tools ill-equipped for ideal assembly. We present CarpeDeam, a novel damage-aware de novo assembler designed specifically for ancient metagenomic samples. Utilizing maximum-likelihood frameworks that integrate sample-specific damage patterns, CarpeDeam demonstrates improved recovery of longer continuous sequences and protein sequences in many simulated and empirical datasets compared to existing assemblers. As a pioneering ancient metagenome assembler, CarpeDeam opens the door for new opportunities in functional and taxonomic analyses of ancient microbial communities.