CarpeDeam: ADe NovoMetagenome Assembler for Heavily Damaged Ancient Datasets
Author:
Kraft LouisORCID, Söding JohannesORCID, Steinegger MartinORCID, Jochheim Annika, Sackett Peter Wad, Fernandez-Guerra AntonioORCID, Renaud GabrielORCID
Abstract
AbstractDe novoassembly 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 presentCarpeDeam, a novel damage-awarede novoassembler designed specifically for ancient metagenomic samples. Utilizing maximum-likelihood frameworks that integrate sample-specific damage patterns,CarpeDeamrecovers longer continuous sequences and more protein sequences from both simulated and empirical datasets compared to existing assemblers. As a pioneering ancient metagenome assembler,CarpeDeamopens the door for new opportunities in functional and taxonomic analyses of ancient microbial communities.
Publisher
Cold Spring Harbor Laboratory
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