Benchmarking short-read metagenomics tools for removing host contamination

文献类型： 外文期刊

第一作者： Gao, Yunyun

作者： Gao, Yunyun;Luo, Hao;Yang, Haifei;Yousuf, Salsabeel;Liu, Yong-Xin;Lyu, Hujie;Yang, Haifei;Huang, Shi

作者机构：

关键词： metagenome; microbiome; host removal; microbial enrichment

期刊名称：GIGASCIENCE （ 影响因子：3.9； 五年影响因子：11.1 ）

ISSN： 2047-217X

年卷期： 2025 年 14 卷

页码：

收录情况： SCI

摘要： Background The rapid evolution of metagenomic sequencing technology offers remarkable opportunities to explore the intricate roles of microbiome in host health and disease, as well as to uncover the unknown structure and functions of microbial communities. However, the swift accumulation of metagenomic data poses substantial challenges for data analysis. Contamination from host DNA can substantially compromise result accuracy and increase additional computational resources by including nontarget sequences.Results In this study, we assessed the impact of computational host DNA decontamination on downstream analyses, highlighting its importance in producing accurate results efficiently. We also evaluated the performance of conventional tools like KneadData, Bowtie2, BWA, KMCP, Kraken2, and KrakenUniq, each offering unique advantages for different applications. Furthermore, we highlighted the importance of an accurate host reference genome, noting that its absence negatively affected the decontamination performance across all tools.Conclusions Our findings underscore the need for careful selection of decontamination tools and reference genomes to enhance the accuracy of metagenomic analyses. These insights provide valuable guidance for improving the reliability and reproducibility of microbiome research.

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