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装配QC:一个Nextflow管道,用于可重复的组装质量报告

Usman Rashid¹, Chen Wu¹, Jason Shiller²

¹Molecular & Digital Breeding, The New Zealand Institute for Plant and Food Research Limited, 1025 Auckland, New Zealand.

Bioinformatics (Oxford, England)

|July 30, 2024

概括

我们开发了AssemblyQC,这是评估基因组组装质量的全面管道. 该工具通过使用先进方法评估连续性,完整性和准确性,确保可靠的下游分析.

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.

背景情况:

基因组组装项目由于测序和组装算法的进步而迅速扩展.
准确的基因组组装质量评估对于可靠的下游分析和生物解释至关重要.

研究的目的:

引入AssemblyQC管道,这是一个全面的基因组组装质量评估的强大工具.
为评估基因组组装质量的各个方面提供标准化和可重复的方法.

主要方法:

AssemblyQC执行文件格式验证,污染物检查,连续性测量和基因/重复空间完整性的量化.
该管道包括端粒检查,分类学分配,合成基对齐和使用Hi-C接触图的支架检查.
K-mer分析用于评估完整性,共识质量和分阶段,生成详细的HTML报告.

主要成果:

装配QC管道将多个质量评估指标集成到一个单一的,用户友好的工作流中.
它提供了详细的报告与可视化和方法描述,以清楚地解释基因组组装质量.

结论:

AssemblyQC为基因组组装质量评估提供了可复制,可扩展和可移植的解决方案.
该管道是使用Nextflow和nf-core最佳实践构建的,可在GitHub上使用,促进可访问性和社区贡献.

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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.