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完全的人类和植物染色体的无间隙组装,仅使用纳米孔测序
Sergey Koren1, Zhigui Bao2,3, Andrea Guarracino4
1Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA; sergey.koren@nih.gov adam.phillippy@nih.gov.
Genome research
|November 6, 2024
概括
牛津纳米孔技术 (ONT) 双重测序为完整的基因组组装提供了一个单一仪器解决方案. 这种方法实现了高精度和连续性,与现有的多平台方法竞争,用于各种物种.
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:
- 端粒对端粒基因组组装以前需要多个测序平台,如牛津纳米孔技术 (ONT) 和太平洋生物科学 (PacBio) 高保真度 (HiFi) 阅读.
- 这种多平台的方法限制了完全基因组重建的可访问性.
- 新兴的ONT双重序列,它可以读取两个DNA链,提供高每基准确性和长读取.
研究的目的:
- 评估ONT双重测序对新基因组组装的有用性.
- 为了评估与PacBio HiFi阅读相比Duplex测序的性能.
- 探索Pore-C染色体接触映射用于哈普罗型分相的使用.
主要方法:
- 生成了人类 (HG002),西红 (Solanum lycopersicum) 和玉米 (Zea mays) 基因组的ONT双重测序数据.
- 利用Pore-C染色体接触映射用于异质合体人类HG002基因组中的单双型分相.
- 使用现有的双体组装算法与Duplex和Pore-C数据.
主要成果:
- ONT双测序显示的准确性与PacBio HiFi读数相当,读数长度明显更长.
- 孔-C数据证明与当前的双倍组装算法兼容.
- 结合方法产生了高度准确的 (>99.999% Q50) 和连续的基因组组件,大多数染色体组装为单个连接.
结论:
- ONT双重测序是PacBio HiFi测序的可行和可访问的替代方案,用于新的基因组组装.
- 现在,一个单一的仪器可以用于多次运行,完整的基因组重建,包括单 haplotype 阶段化.
- 这种进步有助于完成多样化和复杂的基因组.
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