biostudies-literatureKraft LGerman Network for Bioinformatics Infrastructure (de.NBI)Novo Nordisk FondenGerman Network for Bioinformatics Infrastructure372https://www.ebi.ac.uk/biostudies/studies/S-EPMC12557918biostudies-literatureUnknown26(1)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.Genome biologyCarpeDeam: a de novo metagenome assembler for heavily damaged ancient datasets.PMC12557918031A537B, 031A533A, 031A538A, 031A533B, 031A535A, 031A537C, 031A534A, 031A532BNNF20OC0062491Soding JFernandez-Guerra ARenaud GKraft LJochheim AWad Sackett PSteinegger MfalseCarpeDeam: 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.2025-01-01T00:00:00Z2025 Oct2026-06-05T07:53:24.947Z2026-05-14T03:12:55.683ZS-EPMC125579184114629010.1186/s13059-025-03839-5