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追踪并列重复:一个可定制的管道用于识别和跨物种比较

Carolina L Adam¹, Joana Rocha², Peter Sudmant²

¹Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403, United States.

Bioinformatics advances

|May 12, 2025

概括

TRACK是一个用户友好的工作流程,用于发现和比较跨物种的并列重复 (TR). 该工具增强了TR分析的可访问性和可重复性,并集成了对目录,基因型和种群遗传学的功能.

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.
人口遗传学人口遗传学

背景情况:

串联重复 (TR) 是各种生物过程中关键的基因组元素.
发现和比较跨物种的TR是计算上具有挑战性的.
现有的工具缺乏综合功能来进行全面的TR分析.

研究的目的:

开发一个用户友好和集成的工作流程,以有效地发现TR和跨物种的比较.
提高TR分析在基因组学研究中的可访问性和可重复性.
为TRs提供一个灵活的工具,用于编目,基因型和人口遗传分析.

主要方法:

使用Snakemake来实现工作流程自动化.
实现了对应的LiftOver和顺序对齐,用于同类的TR识别.
综合TR编目,过,基因型和人口遗传统计估计.

主要成果:

开发了 TRACK,这是一个简化了用于 TR 分析的 Snakemake 工作流.
TRACK促进了跨物种的TR发现,比较和基因定型.
工作流允许对TRs进行基本人口遗传统计的估计和绘图.

结论:

TRACK提高了并联重复分析的可访问性和可重复性.
集成的工作流提供灵活性,以满足各种基因组研究需求.
TRACK使研究人员能够进行跨物种的全面TR研究.

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