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Levente Zsichla^1,2, Marius Zeeb^3,4, Dávid Fazekas^1,5

¹Institute of Biology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary.

|January 8, 2025

概括

从下一代测序 (NGS) 数据中选择病毒基因组组装的生物信息学管道至关重要. 希弗和SmaltAlign为不同的样本提供了强大的性能,确保精确的病毒基因组重建.

科学领域:

生物信息学和计算生物学
基因组学和遗传学基因组学和遗传学
病毒学和传染病学.

背景情况:

下一代测序 (NGS) 越来越多地用于临床诊断和流行病学.
这就需要有效,自动化和用户友好的生物信息学工作流程来进行病毒基因组组装.
评估现有工具对于指导研究人员选择合适的管道至关重要.

研究的目的:

评估四个开源生物信息管道的性能和适用性,用于从NGS数据中进行全长病毒基因组组装.
用模拟和现实世界HIV-1数据集来比较管道.
根据数据特征和用户需求,为管道选择提供建议.

主要方法:

评估了四个管道:shiver (包括一个Dockerized版本,dshiver),SmaltAlign,viral-ngs和V-pipe.
利用模拟和现实世界HIV-1配对短读数据集与默认设置.
根据质量指标 (基因组分数恢复,不匹配/indel率,变异调用F1分数),运行时间和用户友好性) 评估性能.

主要成果:

所有管道都实现了高质量的共识基因组组合,具有非常相似的参考序列.
什维尔和SmaltAlign在更分散的样本 (不匹配的亚型) 中表现强.
与V-Pipe和shiver相比,SmaltAlign和viral-ngs在实证数据集上的运行时间显著缩短;V-Pipe提供了最广泛的功能,SmaltAlign和dshiver平衡了用户友好性和稳定性,而viral-ngs需要更少的计算资源.

结论:

对于密切匹配的参考序列,所有评估的管道都可靠地重建病毒共识基因组.
管道选择可以由用户友好性和运行时间考虑指导.
对于缺乏匹配参考的分离样本,建议使用shiver或SmaltAlign以获得强大的性能;dshiver提高了shiver的可用性.

关键词:

基准测试 (benchmarking) 是一种比较的方法.生物信息学管道中的一个.基因组组装组合的基因组.这是下一代测序.

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