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全动物基因组测序:用户友好,快速,容器化管道用于处理,变体发现和短读全基因组测序数据的注释

Jonah N Cullen¹, Steven G Friedenberg¹

¹Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota, 1352 Boyd Ave, Saint Paul, MN 55108, USA.

G3 (Bethesda, Md.)

|May 27, 2023

概括

全动物基因组测序 (WAGS) 提供了用户友好的管道,用于识别任何物种的遗传变异. 这种开源工具简化了复杂的生物信息学,使基因组测序更容易用于兽医研究和其他领域.

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.
兽医科学兽医科学兽医科学

背景情况:

短读测序的进步使得跨物种的大规模变异发现成为可能.
处理高通量测序数据给生物信息学带来了挑战,包括可重现性问题.
现有的管道往往缺乏适应非模型生物或跨机构使用的适应性.

研究的目的:

引入全动物基因组测序 (WAGS),一个开源的,容器化的管道套件.
为了简化生殖线短变体 (SNP,indel) 和结构变体 (SV) 的识别.
为任何具有参考基因组的物种提供可适应的用户友好解决方案,特别是为兽医界提供.

主要方法:

根据基因组分析工具包 (GATK) 的最佳实践开发了WAGS管道.
利用容器化,以便在各个机构中轻松配置和可重复性.
适应已建立的生物信息学工作流程,以广泛的物种适用性.

主要成果:

WAGS管道简化了SNP,indel和SV的识别.
基准测试数据显示了预处理和联合基因型化步骤的效率.
该系统的设计是为了用户友好和适应性.

结论:

WAGS为全动物基因组测序提供了强大且易于获得的解决方案.
这些管道有助于在不同物种中发现可复制变异.
这种工具赋予了兽医界和研究人员与非模型生物工作的权力.

关键词:

管道管道管道管道管道管道管道变种变种的变种整个基因组的测序.

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