CarpeDeam: A De Novo Metagenome Assembler for Heavily Damaged Ancient Datasets

Louis Kraft, Johannes Soeding, Martin Steinegger, Annika Jochheim, Antonio Fernandez-Guerra, Gabriel Renaud
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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 recovers longer continuous sequences and more protein sequences from both 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.
CarpeDeam:用于严重破坏的古代数据集的全新元基因组组装器
从头组装古元基因组数据集是一项极具挑战性的任务。超短的片段大小和古DNA分子测序后特有的损伤模式使目前的工具无法实现理想的组装。我们介绍了 CarpeDeam,这是一种专门为古代元基因组样本设计的新型损伤感知从头装配器。与现有的组装器相比,CarpeDeam 利用最大似然框架整合了特定样本的损伤模式,能从模拟和经验数据集中恢复更长的连续序列和更多的蛋白质序列。作为古代元基因组组装器的先驱,CarpeDeam 为古代微生物群落的功能和分类分析打开了新的机遇之门。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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