circtools - a bioinformatics toolbox for circular RNA analysis

• Applicant: Professor Dr. Christoph Dieterich
• Subject Area: Bioinformatics and Theoretical Biology ; Epidemiology and Medical Biometry/Statistics ; Software Engineering and Programming Languages
• Term: since 2021
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 443187912

While several tools for circular RNA prediction exist, publicly available one-stop software suites are virtually absent. To address this need, we developed the circtools software to provide a harmonized workflow that covers different stages of in silico circRNA analyses, from prediction to first functional insights. Circtools is a modular, Python-based framework, which is accessible through a single command line interface. Currently available modules encompass initial sequencing library quality checks, test of circRNAs for host gene independent expression, identify differentially spliced exons, screen circRNAs for enriched features (e.g. RNA binding protein (RBP) binding sites), and design circRNA-specific primers for qRT-PCR verification. Circtools supports researchers with visualization options and data export into commonly used formats. Given that the roots of circtools trace back to different sources, it is our aim to improve quality and maintainability of the code base (Objective 1). Circtools has its roots in two circRNA analysis tools originally written as part of master’s and Ph.D. thesis. Therefore, it is our aim to harmonize the code base of the project and thus reduce potential unintended side effects as well as to ease the implementation of new modules dependent on legacy code. Automatic code tests performed via continuous integration (CI) methods is a fundamental part of these efforts.Circtools in its current version covers all major steps of computational circRNA analysis. However, from own experiments as well as valuable feedback from collaborators, it will be necessary to add new functionality the workflow. Thus, we intent to extend the module repertoire of circtools with additional algorithms, such as modules advanced primer design for linear host genes and assessment of the conservation of circRNA candidate throughout different species (Objective 2). Although we provide a detailed step-by-step documentation and built-in help of circtools, our command line-based approach is still an inhibiting factor for researchers with limited experience of command line tools. As a first step, the primer as well as the siRNA design module will be turned into an additional web application, that allows researchers to easily use both function without the need of command line work or any kind of installation (Objective 3). Additionally, the circtools workflow itself will be adapted for usage within the Galaxy framework to also open the detection workflow to novice users. Finally, the workflow will be covered by video tutorials and workshops (Objective 4).

• DFG Programme: Research Grants