Evaluation of 10 Different Pipelines for Bacterial Single-Nucleotide Variant Detection

IF 2 Q3 INFECTIOUS DISEASES
Zi-Hao Hu, Ying Wang, Long Yang, Qing-Yi Cao, Ming Ling, Xiao-Hua Meng, Yao Chen, Shu-Jun Ni, Zhi Chen, Cheng-Zhi Liu, Kun-Kai Su
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Abstract

Abstract Bacterial genome sequencing is a powerful technique for studying the genetic diversity and evolution of microbial populations. However, the detection of genomic variants from sequencing data is challenging due to the presence of contamination, sequencing errors and multiple strains within the same species. Several bioinformatics tools have been developed to address these issues, but their performance and accuracy have not been systematically evaluated. In this study, we compared 10 variant detection pipelines using 18 simulated and 17 real datasets of high-throughput sequences from a bundle of representative bacteria. We assessed the sensitivity of each pipeline under different conditions of coverage, simulation and strain diversity. We also demonstrated the application of these tools to identify consistent mutations in a 30-time repeated sequencing dataset of Staphylococcus hominis. We found that HaplotypeCaller, but not Mutect2, from the GATK tool set showed the best performance in terms of accuracy and robustness. CFSAN and Snippy performed not as well in several simulated and real sequencing datasets. Our results provided a comprehensive benchmark and guidance for choosing the optimal variant detection pipeline for high-throughput bacterial genome sequencing data.
评估用于细菌单核苷酸变异检测的 10 种不同管道
摘要 细菌基因组测序是研究微生物种群遗传多样性和进化的一项强大技术。然而,由于存在污染、测序错误和同一物种中的多个菌株,从测序数据中检测基因组变异具有挑战性。为了解决这些问题,已经开发了几种生物信息学工具,但尚未对其性能和准确性进行系统评估。在这项研究中,我们使用了 18 个模拟数据集和 17 个真实数据集,对 10 个变异检测管道进行了比较,这些数据集来自一束具有代表性的细菌的高通量序列。我们评估了每种管道在不同覆盖率、模拟和菌株多样性条件下的灵敏度。我们还展示了这些工具在人葡萄球菌 30 次重复测序数据集中识别一致突变的应用。我们发现,GATK 工具集中的 HaplotypeCaller(而非 Mutect2)在准确性和鲁棒性方面表现最佳。CFSAN 和 Snippy 在几个模拟和真实测序数据集中的表现不尽如人意。我们的研究结果为高通量细菌基因组测序数据选择最佳变异检测管道提供了全面的基准和指导。
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