Mutation Detection Software for Bench Scientists
Additional Funding Sources
This project is supported by a 2018-2019 STEM Undergraduate Research Grant from the Higher Education Research Council. The project was also supported by an Institutional Development Award (IDeA) from the National Institute of General Medical Sciences of the National Institutes of Health under Grant #P20GM103408.
Abstract
The accurate detection of bona fide causal DNA mutations in a sequenced sample is critical for gene function discovery studies. The rapid sequencing rate and high-throughput nature of next-generation sequencing (NGS) technologies have greatly accelerated the pace of discoveries in molecular genetics. The computational task of detecting DNA variants in large-scale NGS sequencing datasets may be daunting for the typical bench scientist. In an era of tremendous advances in computing and reliable cyberinfrastructure availability, empowering wet-lab scientists to independently perform computational analysis on sequencing datasets without the requirement for detailed knowledge of the underlying hardware and software infrastructure is a very desirable goal. We describe the initial implementation of a user-friendly DNA variant-detection software for the analysis of NGS sequencing datasets called Variant-Scope. Variant-Scope is implemented in Python and provides an intuitive user-interface (UI), and also includes a setup configuration wizard, computation status viewer, and a variety of summary charts and figures generated for an experimental study. Variant-Scope integrates cutting-edge NGS analysis software suites such as BWA (for reads alignment), SAMtools (for variant detection), BEDTools (for genome arithmetic), and SnpEff (for variant-effect annotation), and is distributed as a package for users running Windows, MacOS, or Linux. Variant-Scope is a very flexible package and can handle sequencing datasets ranging from whole-genome sequences of single individuals to large populations. The package is freely available and has been successfully utilized for the detection of both Fast-Neutron and EMS-induced DNA variants in a variety of mutagenized populations.
Mutation Detection Software for Bench Scientists
The accurate detection of bona fide causal DNA mutations in a sequenced sample is critical for gene function discovery studies. The rapid sequencing rate and high-throughput nature of next-generation sequencing (NGS) technologies have greatly accelerated the pace of discoveries in molecular genetics. The computational task of detecting DNA variants in large-scale NGS sequencing datasets may be daunting for the typical bench scientist. In an era of tremendous advances in computing and reliable cyberinfrastructure availability, empowering wet-lab scientists to independently perform computational analysis on sequencing datasets without the requirement for detailed knowledge of the underlying hardware and software infrastructure is a very desirable goal. We describe the initial implementation of a user-friendly DNA variant-detection software for the analysis of NGS sequencing datasets called Variant-Scope. Variant-Scope is implemented in Python and provides an intuitive user-interface (UI), and also includes a setup configuration wizard, computation status viewer, and a variety of summary charts and figures generated for an experimental study. Variant-Scope integrates cutting-edge NGS analysis software suites such as BWA (for reads alignment), SAMtools (for variant detection), BEDTools (for genome arithmetic), and SnpEff (for variant-effect annotation), and is distributed as a package for users running Windows, MacOS, or Linux. Variant-Scope is a very flexible package and can handle sequencing datasets ranging from whole-genome sequences of single individuals to large populations. The package is freely available and has been successfully utilized for the detection of both Fast-Neutron and EMS-induced DNA variants in a variety of mutagenized populations.
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