通过核酸改性和基于参考的校正来纠正纳米孔测序中的修改中介错误
Chien-Shun Chiou1, Bo-Han Chen1, You-Wun Wang1
1Centers for Disease Control, Taichung, Taiwan.
Communications biology
|November 29, 2023
概括
新型DNA修改可以降低牛津纳米孔技术 (ONT) 测序质量. 一种名为Modpolish的新方法纠正了这些错误,同时保留了表观基因组数据,改善了内部和公共数据集.
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:
- 牛津纳米孔技术 (ONT) 测序精度随着流细胞,套件和基调的进步而得到改善.
- 然而,新型DNA修改未被基调调用模型识别,可能会显著降低序列质量.
研究的目的:
- 调查新型修改类型对ONT测序质量的影响.
- 开发和评估纠正修改诱导错误的方法,同时保留表观基因组信息.
主要方法:
- 全基因组放大用于改造.
- 开发Modpolish,一种基于引用的方法来纠正修改错误.
- 在内部和公共ONT数据集上对Modpolish的评估 (R9.4和R10.4简单).
主要成果:
- 新型修改类型被确定为ONT测序基因组中意想不到的低质量的原因.
- 通过全基因组放大进行脱变,提高了质量,但导致了表观基因组损失.
- Modpolish有效地纠正了修改中介错误,保留了表观基因组数据,并在各种数据集中改善了质量.
结论:
- 新的DNA修改是ONT测序中的系统错误的重要来源.
- 这些错误可以使用核酸去修改或Modpolish方法进行纠正,即使没有事先了解这些修改.
- Modpolish提供了一种有价值的解决方案,可以提高ONT数据质量,同时保留关键的表观基因组信息.
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