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Pipeasm:一种用于自动化大染色体规模基因组组装和评估的工具

Bruno Marques Silva¹, Fernanda de Jesus Trindade¹, Lucas Eduardo Costa Canesin¹

¹Environmental Genomics, Instituto Tecnológico Vale, Belém, Pará 66055-090, Brazil.

Bioinformatics advances

|January 16, 2026

概括

Pipeasm是一个新的自动化基因组组装管道,使用容器化工作流简化了这个过程. 该工具提高了从各种数据类型中生成高质量的染色体规模基因组组件的可复制性和效率.

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:

组装大型基因组是复杂的,需要大量的资源.
需要用于基因组组装的自动化和可重复的工作流程.

研究的目的:

为了介绍Pipeasm,一个自动化的基因组组装管道.
简化创建高质量的染色体规模基因组组件的过程.

主要方法:

Pipeasm使用Snakemake和Singularity进行集装箱化工作流管理.
该管道集成了各种数据类型,包括HiFi,ONT和Hi-C读取.
自动化步骤包括读取修剪,核和线粒基因组组装,脚手架,消毒和质量评估.

主要成果:

Pipeasm为四种脊椎动物物种生成了高质量的基因组组件.
会议展示了与基因组大小成比例的支架L50和高达99.6%的BUSCO完整性.
该管道提供了详细的报告,基因组统计数据和Hi-C地图.

结论:

Pipeasm为基因组组装提供了一种高效,可复制和自动化的解决方案.
管道具有适应性,并支持未来的装配标准更新.
Pipeasm为各种物种提供高质量的基因组组件.

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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.