GenomeQC: a quality assessment tool for genome assemblies and gene structure annotations
GenomeQC: a quality assessment tool for genome assemblies and gene structure annotations
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DOI：
10.1186/s12864-020-6568-2
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发表时间：
2020-03-02
期刊：
影响因子：
4.4
通讯作者：
Hufford, Matthew B.
中科院分区：
文献类型：
--
作者：
Manchanda, Nancy;Portwood, John L., II;Hufford, Matthew B.
背景基因组组装是理解物种生物学的基础。它们提供了一个物理框架，用于绘制额外的序列，从而能够表征，例如，基因组多样性和个体和组织类型之间的基因表达差异。基因组组装的质量指标衡量组装的完整性和连续性，并帮助提供下游生物学见解的信心。为了比较多个组装体的质量，通常计算一组通用度量，然后将其与一个或多个金标准参考基因组进行比较。虽然有几个工具用于计算个别指标，应用程序提供多个组件功能的综合评估，也许令人惊讶的是，缺乏。在这里，我们描述了一个新的工具包，它集成了多个指标来表征组装和基因注释质量的方式，使多个组件和组装types.ResultsOur应用程序，名为GenomeQC，是一个易于使用的和交互式的Web框架，集成了各种定量措施来表征基因组组装和注释。GenomeQC为研究人员提供了这些统计数据的全面总结，并允许对金标准参考assemblies.ConclusionsThe GenomeQC Web应用程序在R/Shiny版本1.5.9和Python 3.6中实现，并在GPL许可下在https://genomeqc.maizegdb.org/上免费提供。GenomeQC管道的所有源代码和容器化版本都可以在GitHub存储库https://github.com/HuffordLab/GenomeQC中找到。
BackgroundGenome assemblies are foundational for understanding the biology of a species. They provide a physical framework for mapping additional sequences, thereby enabling characterization of, for example, genomic diversity and differences in gene expression across individuals and tissue types. Quality metrics for genome assemblies gauge both the completeness and contiguity of an assembly and help provide confidence in downstream biological insights. To compare quality across multiple assemblies, a set of common metrics are typically calculated and then compared to one or more gold standard reference genomes. While several tools exist for calculating individual metrics, applications providing comprehensive evaluations of multiple assembly features are, perhaps surprisingly, lacking. Here, we describe a new toolkit that integrates multiple metrics to characterize both assembly and gene annotation quality in a way that enables comparison across multiple assemblies and assembly types.ResultsOur application, named GenomeQC, is an easy-to-use and interactive web framework that integrates various quantitative measures to characterize genome assemblies and annotations. GenomeQC provides researchers with a comprehensive summary of these statistics and allows for benchmarking against gold standard reference assemblies.ConclusionsThe GenomeQC web application is implemented in R/Shiny version 1.5.9 and Python 3.6 and is freely available at https://genomeqc.maizegdb.org/ under the GPL license. All source code and a containerized version of the GenomeQC pipeline is available in the GitHub repository https://github.com/HuffordLab/GenomeQC.