Comprehensive Evaluation of Genome Gap-Filling Tools Utilizing Long Reads

文献类型： 外文期刊

第一作者： Zhao, Xianjia

作者： Zhao, Xianjia;Liu, Fang;Zhao, Xianjia;Pan, Weihua;Liu, Fang

作者机构：

关键词： gap-filling; long reads; genome assembly

期刊名称：GENES （ 影响因子：3.5； 五年影响因子：3.9 ）

ISSN：

年卷期： 2024 年 15 卷 1 期

页码：

收录情况： SCI

摘要： The availability of the complete genome of an organism plays a crucial role in the comprehensive analysis of the entire biological entity. Despite the rapid advancements in sequencing technologies, the inherent complexities of genomes inevitably lead to gaps during genome assembly. To obviate this, numerous genome gap-filling tools utilizing long reads have emerged. However, a comprehensive evaluation of these tools is currently lacking. In this study, we evaluated seven software under various ploidy levels and different data generation methods, and assessing them using QUAST and two additional criteria such as accuracy and completeness. Our findings revealed that the performance of the different tools varied across diverse ploidy levels. Based on accuracy and completeness, FGAP emerged as the top-performing tool, excelling in both haploid and tetraploid scenarios. This evaluation of commonly used genome gap-filling tools aims to provide users with valuable insights for tool selection, assisting them in choosing the most suitable genome gap-filling tool for their specific needs.

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