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CLAW:一种自动化的Snakemake工作流程,用于从长时间读取的数据中组装叶绿体基因组

Aaron L Phillips¹, Scott Ferguson², Rachel A Burton¹

¹Department of Food Science, University of Adelaide, Adelaide, South Australia, Australia.

PLoS computational biology

|February 9, 2024

概括

CLAW是一个新的工作流工具,它简化了从长期读取的测序数据中进行质体基因组组装. 这种工具使研究人员能够有效地生成高质量的叶绿体基因组组件,帮助进化和作物改进研究.

科学领域:

植物科学植物科学
基因组学就是基因组学.
生物信息学是一种生物信息学.

背景情况:

叶绿体基因组对于进化研究,分类学和作物改进至关重要.
在DNA测序方面的进步在全基因组图书馆中产生了丰富的 хлоропласт基因组数据.
现有的组装工具可能很复杂,缺乏可扩展性.

研究的目的:

介绍CLAW,一个用户友好的Snakemake工作流程,用于组装叶绿体基因组.
从全基因组库中的长时间读取数据中实现高效的叶绿体基因组组装.

主要方法:

开发了基于Snakemake的CLAW工作流程,用于质体基因组组装.
利用来自全基因组库的长读测序数据.
使用来自不同物种的19个公共参考叶绿体基因组测试了CLAW.

主要成果:

CLAW迅速产生了与参考基因组高度相似的叶绿体基因组组.
该工作流程在藻类,单种藻类和藻类物种中表现出有效性.
CLAW为特定应用程序提供了用户对参数化的控制.

结论:

CLAW为质细胞基因组组装提供了一个可访问和可扩展的解决方案.
该工具有助于扩展公开可用的叶绿体基因组数据集.
具有不同生物信息学专业知识的研究人员可以利用CLAW进行研究.

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Genome Annotation and Assembly

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.