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bioRxiv · 10.1101/2024.08.09.607291

CarpeDeam: A De Novo Metagenome Assemblerfor Heavily Damaged Ancient Datasets

Kraft, L.·Soeding, J.·Steinegger, M.·Jochheim, A.·Fernandez-Guerra, A.·Renaud, G.
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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.

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Kraft, L., Soeding, J., Steinegger, M., Jochheim, A., Fernandez-Guerra, A., Renaud, G.. 2024-08-09. CarpeDeam: A De Novo Metagenome Assemblerfor Heavily Damaged Ancient Datasets. https://doi.org/10.1101/2024.08.09.607291

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