CarpeDeam: a de novo metagenome assembler for heavily damaged ancient datasets
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.
Authors
- Johannes Söding (ORCID: https://orcid.org/0000-0001-9642-8244)
- Gabriel Renaud (ORCID: https://orcid.org/0000-0002-0630-027X)
- Antonio Fernàndez-Guerra (ORCID: https://orcid.org/0000-0002-8679-490X)
- Annika Jochheim (ORCID: https://orcid.org/0000-0001-6791-9167)
- Peter Wad Sackett (ORCID: https://orcid.org/0000-0003-3628-2807)
- Louis Kraft (ORCID: https://orcid.org/0000-0002-6465-4973)
- Martin Steinegger
Institutions
- University of Copenhagen (DK)
- Seoul National University (KR)
- Sustainability Institute (ZA)
- International Max Planck Research School for Advanced Methods in Process and Systems Engineering (DE)
- Université Laval (CA)
- Max Planck Institute for Multidisciplinary Sciences (DE)
- University of Göttingen (DE)
- Technical University of Denmark (DK)
Publication Details
- Journal
- Genome biology
- Published
- 2025-10-27
- DOI
- https://doi.org/10.1186/s13059-025-03839-5
- Citations
- 1
- Primary Topic
- Forensic and Genetic Research
- Type
- article
- Field-Weighted Citation Impact
- 1.82
Funders
- National Research Foundation
- Danmarks Grundforskningsfond
- Bundesministerium für Bildung und Forschung
- Novo Nordisk
- Danmarks Tekniske Universitet
- Novo Nordisk Fonden
- German Network for Bioinformatics Infrastructure