{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Kraft L"],"funding":["German Network for Bioinformatics Infrastructure (de.NBI)","Novo Nordisk Fonden","German Network for Bioinformatics Infrastructure"],"pagination":["372"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC12557918"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["26(1)"],"pubmed_abstract":["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."],"journal":["Genome biology"],"pubmed_title":["CarpeDeam: a de novo metagenome assembler for heavily damaged ancient datasets."],"pmcid":["PMC12557918"],"funding_grant_id":["031A537B, 031A533A, 031A538A, 031A533B, 031A535A, 031A537C, 031A534A, 031A532B","NNF20OC0062491"],"pubmed_authors":["Soding J","Fernandez-Guerra A","Renaud G","Kraft L","Jochheim A","Wad Sackett P","Steinegger M"],"additional_accession":[]},"is_claimable":false,"name":"CarpeDeam: a de novo metagenome assembler for heavily damaged ancient datasets.","description":"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.","dates":{"release":"2025-01-01T00:00:00Z","publication":"2025 Oct","modification":"2026-06-05T07:53:24.947Z","creation":"2026-05-14T03:12:55.683Z"},"accession":"S-EPMC12557918","cross_references":{"pubmed":["41146290"],"doi":["10.1186/s13059-025-03839-5"]}}