Abstract Modern DNA sequencing has instituted a new era in human cytomegalovirus (HCMV) genomics. A key development has been the ability to determine the genome sequences of HCMV strains directly from clinical material. This involves the application of complex and often non-standardized bioinformatics approaches to analysing data of variable quality in a process that requires substantial manual intervention. To relieve this bottleneck, we have developed GRACy (Genome Reconstruction and Annotation of Cytomegalovirus), an easy-to-use toolkit for analysing HCMV sequence data. GRACy automates and integrates modules for read filtering, genotyping, genome assembly, genome annotation, variant analysis, and data submission. These modules were tested extensively on simulated and experimental data and outperformed generic approaches. GRACy is written in Python and is embedded in a graphical user interface with all required dependencies installed by a single command. It runs on the Linux operating system and is designed to allow the future implementation of a cross-platform version. GRACy is distributed under a GPL 3.0 license and is freely available at https://bioinformatics.cvr.ac.uk/software/ with the manual and a test dataset.

中文翻译：

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GRACY：分析人类巨细胞病毒序列数据的工具

摘要 现代 DNA 测序开创了人类巨细胞病毒 (HCMV) 基因组学的新纪元。一个关键的发展是能够直接从临床材料中确定 HCMV 毒株的基因组序列。这涉及在需要大量人工干预的过程中应用复杂且通常非标准化的生物信息学方法来分析质量可变的数据。为了缓解这一瓶颈，我们开发了 GRACy（巨细胞病毒基因组重建和注释），这是一个易于使用的工具包，用于分析 HCMV 序列数据。GRACy 自动化并集成了用于读取过滤、基因分型、基因组组装、基因组注释、变异分析和数据提交的模块。这些模块在模拟和实验数据上进行了广泛的测试，并且优于通用方法。GRACy 是用 Python 编写的，并嵌入在图形用户界面中，所有必需的依赖项都通过单个命令安装。它在 Linux 操作系统上运行，旨在允许未来实现跨平台版本。GRACy 在 GPL 3.0 许可下分发，可在 https://bioinformatics.cvr.ac.uk/software/ 上免费获得手册和测试数据集。