Genomics Division, National Institute of Agricultural Science, 370 Nongsaengmyeong-ro, Jeonju, 54874, Republic of Korea.
Interdisciplinary Program in Bioinformatics, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.
Genes Genomics. 2020 Nov;42(11):1311-1317. doi: 10.1007/s13258-020-00997-7. Epub 2020 Sep 26.
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.
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.
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).
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.
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.
序列变异，如单核苷酸多态性，是遗传疾病和繁殖的标记。因此，识别序列变异是几个基因组项目的主要目标之一。尽管大多数基因组项目联盟都为序列变异检测方法提供了标准操作程序，但由于人为选择或错误，结果可能存在差异。
为了规范序列变异检测程序，并帮助那些没有接受过生物信息学正式培训的研究人员，我们开发了 NGS_SNPAnalyzer，这是一款桌面软件和完全自动化的图形化流程。
NGS_SNPAnalyzer 是使用 JavaFX（版本 1.8）实现的；因此，它不受任何操作系统（OS）的限制。NGS_SNPAnalyzer 中使用的工具是在 Microsoft Windows（版本 7、10）和 Ubuntu Linux（版本 16.04、17.0.4）上编译的。
NGS_SNPAnalyzer 不仅包括变异调用和注释的功能，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流程。它可以使用预定义的管道和选项执行，并通过用户指定的选项进行定制。此外，NGS_SNPAnalyzer 提供了用户友好的图形界面，可以在支持 JAVA 的任何操作系统上安装。
尽管有几个用于 NGS 数据分析的管道和可视化工具，但我们开发了 NGS_SNPAnalyzer 为用户提供了一个易于使用的界面。基准测试结果表明，NGS_SNPAnayzer 的性能优于其他开源工具。
