Background

Sequence variations such as single nucleotide polymorphisms are markers for genetic diseases and breeding. Therefore, identifying sequence variations is one of the main objectives of several genome projects. Although most genome project consortiums provide standard operation procedures for sequence variation detection methods, there may be differences in the results because of human selection or error.

Objective

To standardize the procedure for sequence variation detection and help researchers who are not formally trained in bioinformatics, we developed the NGS_SNPAnalyzer, a desktop software and fully automated graphical pipeline.

Methods

The NGS_SNPAnalyzer is implemented using JavaFX (version 1.8); therefore, it is not limited to any operating system (OS). The tools employed in the NGS_SNPAnalyzer were compiled on Microsoft Windows (version 7, 10) and Ubuntu Linux (version 16.04, 17.0.4).

Results

The NGS_SNPAnalyzer not only includes the functionalities for variant calling and annotation but also provides quality control, mapping, and filtering details to support all procedures from next-generation sequencing (NGS) data to variant visualization. It can be executed using pre-set pipelines and options and customized via user-specified options. Additionally, the NGS_SNPAnalyzer provides a user-friendly graphical interface and can be installed on any OS that supports JAVA.

Conclusions

Although there are several pipelines and visualization tools available for NGS data analysis, we developed the NGS_SNPAnalyzer to provide the user with an easy-to-use interface. The benchmark test results indicate that the NGS_SNPAnayzer achieves better performance than other open source tools.

中文翻译：

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NGS_SNPAnalyzer：通过识别和可视化来自下一代测序数据的序列变异来支持基因组项目的桌面软件

背景

单核苷酸多态性等序列变异是遗传疾病和育种的标志。因此，识别序列变异是几个基因组计划的主要目标之一。尽管大多数基因组计划联盟提供了序列变异检测方法的标准操作程序，但由于人为选择或错误，结果可能存在差异。

客观的

为了标准化序列变异检测程序并帮助未受过正式生物信息学培训的研究人员，我们开发了 NGS_SNPAnalyzer ，这是一款桌面软件和全自动图形管道。

方法

NGS_SNPAnalyzer 是使用 JavaFX（版本 1.8）实现的；因此，它不限于任何操作系统 (OS)。NGS_SNPAnalyzer 中使用的工具在 Microsoft Windows（版本 7、10）和 Ubuntu Linux（版本 16.04、17.0.4）上编译。

结果

NGS_SNPAnalyzer 不仅包括变异调用和注释功能，还提供质量控制、映射和过滤细节，以支持从下一代测序 (NGS) 数据到变异可视化的所有程序。它可以使用预设的管道和选项执行，并通过用户指定的选项进行定制。此外，NGS_SNPAnalyzer 提供了一个用户友好的图形界面，可以安装在任何支持 JAVA 的操作系统上。

结论

尽管有多种管道和可视化工具可用于 NGS 数据分析，但我们开发了 NGS_SNPAnalyzer 来为用户提供易于使用的界面。基准测试结果表明，NGS_SNPAnayzer 的性能优于其他开源工具。