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科罗拉:一个Snakemake工作流程,用于完成染色体规模的新基因组组装

Lia Obinu^1,2, Timothy Booth², Heleen De Weerd²

¹Department of Agricultural Sciences, University of Sassari, Viale Italia 39/a, Sassari, Sardinia, 07100, Italy.

Bioinformatics (Oxford, England)

|April 16, 2025

概括

一个新的自动化工作流程,Colora,简化了生物多样性研究的新基因组组装. 这条Snakemake管道从各种测序数据中确保了高质量,可复制的基因组和器官组件.

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.
计算生物学计算生物学

背景情况:

基因组组装对生物多样性和保护研究至关重要,全球许多实验室正在生成新的参考基因组.
需要一个标准化的,自动化的工作流程来确保数据质量的一致性,并防止在基因组组装中重复努力.

研究的目的:

为了介绍Colora,一个自动化,便携式的工作流程,用于新的基因组组装.
为研究人员提供一个用户友好和可复制的管道,用于生成高质量的基因组组件.

主要方法:

开发了Colora作为一个Snakemake工作流程.
设计用于处理太平洋生物科学HiFi,Hi-C和牛津纳米孔技术测序读取.
能够生产染色体规模的初级或分阶段基因组组件,包括器官.

主要成果:

介绍了Colora,一个多功能和可复制的de novo基因组组装管道.
工作流成功地生成了带有有机细胞基因组的染色体规模组件.
科罗拉是用户友好的,并准备好在研究环境中实施.

结论:

科罗拉为新的基因组组装提供了一种最佳实践,自动化解决方案.
工作流提高了基因组学研究中的可复制性和数据质量.
促进生物多样性和保护工作的高效基因组组装.

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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.