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Evgeniy Mozheiko¹, Heng Yi¹, Anzhi Lu²

¹MGI Tech, Shenzhen 518083, China.

|March 28, 2025

概括

我们发现,牛津纳米孔技术 (ONT) 测序读取,通过下一代测序 (NGS) 进行校正,可以实现与更昂贵的混合方法相匹配的基因组组装性能. 这种方法为基因组组装提供了具有成本效益的替代方案,而无需针对完整的端粒到端粒序列.

科学领域:

基因组学和生物信息学
分子生物学分子生物学

背景情况:

最近测序技术的进步使得端粒对端粒 (T2T) 基因组组装成为可能.
目前的T2T组装方法通常需要大量的太平洋生物科学 (PacBio) HiFi和牛津纳米孔技术 (ONT) 测序数据,增加成本.
第三代测序技术在读数长度和准确性方面不断改进.

研究的目的:

为了研究基因组组装的可行性,使用低覆盖量测序数据.
为了评估ONT的性能,通过下一代测序 (NGS) 校正的读数用于基因组组装.
为了降低基因组组装的总体成本.

主要方法:

使用ONT读数对NGS进行校正的评估平分体基因组组合.
基于ONT的组装与使用PacBio HiFi阅读的混合方法的比较性能指标.
在低覆盖条件下评估了最先进的混合组装器 (Verkko,Hifiasm) 和ONT组装器 (Shasta,Flye).
分析了MGI,Illumina和stLFR NGS技术,用于预组装校正,哈普洛型分相和抛光.

主要成果:

通过NGS校正的ONT-based组件实现了与更昂贵的混合方法相比的性能.
即使使用单一的T2T组件,Verkko和Hifiasm在中心区域也表现出显著的错组件.
MGI,Illumina和stLFR NGS技术在混合基因组组装管道中的实用性得到了严格的评估.

结论:

在T2T完整性不是主要目标时,建议将常规R9或简单R10 ONT读数和准确的NGS读数结合起来进行基因组组装.
这种方法为实现高质量的基因组组件提供了具有成本效益的策略.
通过NGS纠正的基于ONT的组装为昂贵的混合方法提供了可行的替代方案.

关键词:

这就是HiFi,HiFi.在MGI中,MGI是MGI.国家货币体系 (NGS) 修正在线播放在线播放混合组件组件组合混合组件组合组合组合组合组合组合组合组合组合组合组合组合组合组低覆盖范围的组件组合.

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