基因组组装工具的比较,用于使用混合测序技术对Mycobacterium tuberculosis基因组进行表征
Kanwara Trisakul1,2, Yothin Hinwan1,2, Jukgarin Eisiri2
1Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.
PeerJ
|September 2, 2024
概括
使用短读和长读的混合基因组组装提高了Mycobacterium结核病基因组的完整性和基因检测. 这种方法有助于识别用于控制结核病的耐药性突变.
科学领域:
- 基因组学就是基因组学.
- 微生物学 微生物学
- 生物信息学是一种生物信息学.
背景情况:
- 结核菌 (Mtb) 的下一代测序 (NGS) 提高了对基因组多样性和耐药性突变的理解.
- 对Mtb基因组的新组装对于表征循环血统和菌株类型至关重要.
研究的目的:
- 为了比较Unicycler,RagOut和RagTag基因组组装工具对Mtb的性能.
- 使用短读 (Illumina) 和长读 (ONT,PacBio) 测序数据评估混合组装策略.
主要方法:
- 在来自Illumina,ONT和PacBio平台的Mtb序列数据上对Unicycler,RagOut和RagTag组装器进行比较分析.
- 评估基因组完整性,组件大小和跨不同工具和测序技术的连续性.
- 全基因组分析以评估混合组件中的基因检测和SNP识别.
主要成果:
- 单环组件实现了高基因组完整性 (~98.7%).
- 拉格奥特组件导致显著更长的基因组大小和更少的结合物,被选择用于下游分析.
- 混合组件,特别是Illumina和PacBio,检测到的基因 (4,639) 比参考基因 (3,976) 多.
- 所有混合组件都成功识别了与多药耐药结核病 (MDR-TB) 和前广泛耐药结核病 (XDR-TB) 相关的已知突变.
结论:
- 单环机在产生连续的Mtb基因组方面表现出色.
- RagOut通过增加基因组大小来提高组装质量,补充了Unicycler的连续性.
- 短读和长读混合组合提供优越的基因组完整性和基因/SNP检测,与单独短读相比,有助于识别药物耐药性标志物.
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