介绍和对pyMLST的基准测试:使用核心基因组MLST评估细菌克隆性的开源软件
Adrien Biguenet1,2, Augustin Bordy2, Alban Atchon3
1CHU de Besançon, Hygiène Hospitalière, F-25030 Besançon, France.
Microbial genomics
|November 15, 2023
概括
我们介绍pyMLST,一种用于细菌核心基因组多部位序列类型 (cgMLST) 的免费和开源管道. 它的性能与商业软件相似,并且优于其他用于cgMLST分析的开源工具.
科学领域:
- 微生物学 微生物学
- 生物信息学是一种生物信息学.
- 基因组学就是基因组学.
背景情况:
- 全基因组测序 (WGS) 的可负担性增加了核心基因组多部位测序类型 (cgMLST) 的流行,用于细菌类型.
- 目前用于cgMLST分析的工具在性能和可访问性方面各不相同.
研究的目的:
- 推出pyMLST,一个新的,全面的,独立的,免费的,开源的管道用于cgMLST分析.
- 评估pyMLST及其变体pyMLST-KMA的性能,与其他已建立的cgMLST工具相比.
主要方法:
- 开发了pyMLST管道,用于创建/导入cgMLST数据库,使用BLAT/MAFT对准基因,并在SQLite数据库中存储数据.
- 输入选项包括组装的基因组或原始测序数据 (pyMLST-KMA).
- 与pyMLST,pyMLST-KMA,ChewBBACA,SeqSphere进行比较,并使用*Escherichia coli*,*Pseudomonas aeruginosa*和*Staphylococcus aureus*的基因组集合进行变异调用方法.
主要成果:
- pyMLST表现出与商用SeqSphere软件相提并论的性能.
- pyMLST的性能优于其他开源工具,例如ChewBBACA和pyMLST-KMA.
- pyMLST-KMA被确定为大型细菌收集的有用选方法,减少了组装的需要.
结论:
- pyMLST是一个高效,可访问和开源的工具,用于cgMLST分析.
- 管道的性能使其成为细菌类型和疫情调查的宝贵资产.
- pyMLST可以在Galaxy上使用,也可以作为管道准备的工具.
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