进步的仙人掌是一个千基因组时代的多基因组对齐器
Joel Armstrong1, Glenn Hickey1, Mark Diekhans1
1UC Santa Cruz Genomics Institute, UC Santa Cruz, Santa Cruz, CA, USA.
Nature
|November 12, 2020
概括
由于测序数据的快速增加,需要新的基因组分析方法. 进步的仙人掌使得数千个脊椎动物基因组的大规模,无参考对齐具有高准确性.
科学领域:
- 基因组学
- 生物信息学
- 计算生物学
背景情况:
- 测序成本有所下降,第三代技术有所改善,导致新基因组组件的快速增长.
- 在2018年7月至2019年7月期间,脊椎动物基因组组合增加了50% (至1485个).
- 新的人类de novo组件允许分析小的多态和大的结构差异.
研究的目的:
- 解决前所未有规模的基因组数据所带来的挑战.
- 调整现有的基因组分析方法以增加数据规模.
- 开发一个可扩展的多个基因组对齐程序.
主要方法:
- 逐步扩展了无参考多重基因组对齐工具的CACTUS项目.
- 这项改进的程序, Progressive Cactus, 旨在处理成千上万的大型脊椎动物基因组.
- 这种方法在600多个胚胎基因组上进行了测试.
主要成果:
- 进步的仙人掌使得数以万计的大脊椎动物基因组的无参考对齐成为可能.
- 即使有大量的基因组, 该程序也保持了高对齐质量.
- 这项研究产生了迄今为止最大的多个脊椎动物基因组对齐,超过600个胚胎基因组.
结论:
- 渐进性仙人掌克服了以前多个基因组对齐方法的可扩展性限制.
- 开发的方法有助于对大规模的基因组数据进行分析,从而为基因组进化提供了新的见解.
- 这一进步支持了成千上万个基因组的分析,
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