Abstract
BackgroundSequence 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.ObjectiveTo 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.MethodsThe 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).ResultsThe 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.ConclusionsAlthough 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.
Highlights
Massive parallel sequencing has been successful in identifying causal genes of some diseases by detecting sequence variation
To support the detection of sequence variations, the variant detection procedures are implemented as a standard operation procedure (SOP), and the corresponding consortium provides a shell script
Galaxy (Goecks et al 2010) and CLC genomics workbench provide the user with easy-to-use graphical user interfaces (GUIs)
Summary
Massive parallel sequencing has been successful in identifying causal genes of some diseases by detecting sequence variation. In spite of the rush in the development of pipelines and integrated environments, each has their own strengths and limitations (Table 1) Sequence variations such as single nucleotide polymorphisms are markers for genetic diseases and breeding. Results The NGS_SNPAnalyzer includes the functionalities for variant calling and annotation and 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. Conclusions 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
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