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三轮读取校正显著改善了ONT读取中的真核蛋白检测

Hussain A Safar¹, Fatemah Alatar², Abu Salim Mustafa³

¹OMICS Research Unit, Health Science Centre, Kuwait University, Kuwait City 13110, Kuwait.

|February 24, 2024

概括

读取校正工具显著改善了真核生物基因组组合中的基因检测和蛋白质注释,提高了数据的整体质量,而不仅仅是完整性. 这对于准确的物种识别和功能基因分析至关重要.

科学领域:

基因组学就是基因组学.
生物信息学是一种生物信息学.
分子生物学分子生物学

背景情况:

全基因组测序对于真核生物物种识别,基因检测和蛋白质注释至关重要.
牛津纳米孔技术 (ONT) 提供快速,负担得起的真核体测序,但需要先进的生物信息学来解决更高的错误率,以实现精确的基因组组装.

研究的目的:

评估不同读取校正工具对真核生物基因组完整性,基因检测和蛋白质注释的影响.
为了确定读取校正策略是否提高了使用ONT数据的基因组组装的准确性.

主要方法:

ONT从四种真核生物 (C. 阿尔比卡人,C.阿尔比卡人盖蒂,S.S. 的时间谷类植物,P. falciparum) 使用minimap2.2进行组装.
应用了三轮阅读校正,使用飞机,medaka和 racon.
使用 QUAST,BUSCO,BRAKER1 和 InterProScan 来评估组装质量,以确定完整性,基因检测和蛋白质注释.

主要成果:

基因组的完整性更多地取决于组装方法,而不是读取校正工具;medaka表现出卓越的性能.
在基因检测方面,Racon显著超过了Fly和Medaka.
与flye.com相比,Racon和medaka显示出明显更好的蛋白质注释.

结论:

三轮读取校正大大影响了基因检测和蛋白质注释.
组装质量,而不是单纯的完整性,是阅读校正后准确的功能注释的关键.

关键词:

在线播放 ONT ONT ONT 它们是真核生物 (eukaryotes).基因检测基因检测基因检测蛋白质注释蛋白质注释阅读纠正校正阅读纠正

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