circtools - a bioinformatics toolbox for circular RNA analysis

虽然存在几种用于循环RNA预测的工具，但公开可用的一站式软件套件几乎是空白。为了满足这一需求，我们开发了CircTools软件，以提供一个协调的工作流程，涵盖计算机CircRNA分析的不同阶段，从预测到第一次功能洞察。CircTools是一个模块化的、基于Python的框架，可通过单个命令行界面访问。目前可用的模块包括初始测序文库质量检查，检测CircRNAs的宿主基因独立表达，鉴定差异剪接外显子，筛选CircRNAs的丰富特征(例如，RNA结合蛋白(RBP)结合位点)，以及设计CircRNA特异的引物用于qRT-PCR验证。CircTools为研究人员提供可视化选项，并将数据导出为常用格式。鉴于CircTool的根源可以追溯到不同的来源，我们的目标是提高代码库的质量和可维护性(目标1)。CircTools起源于两个CircRNA分析工具，最初是作为硕士和博士论文的一部分编写的。因此，我们的目标是协调项目的代码库，从而减少潜在的意外副作用，并简化依赖于遗留代码的新模块的实现。通过连续集成(CI)方法执行的自动代码测试是这些工作的基本部分。CircTools当前版本涵盖了计算CircRNA分析的所有主要步骤。然而，从自己的实验和合作者的宝贵反馈来看，有必要在工作流中添加新的功能。因此，我们打算用额外的算法来扩展CircTool的模板库，例如用于线性宿主基因的模块高级引物设计和对不同物种中CircRNA候选序列的保守性的评估(目标2)。尽管我们提供了详细的逐步文档和CircTools的内置帮助，但我们基于命令行的方法仍然是对具有有限命令行工具经验的研究人员的制约因素。作为第一步，该引物以及siRNA设计模块将被变成一个额外的网络应用程序，使研究人员无需命令行工作或任何类型的安装即可轻松使用这两种功能(目标3)。此外，CircTools工作流程本身将被调整为在Galaxy框架内使用，以便也向新手用户开放检测工作流程。最后，将通过视频教程和讲习班介绍工作流程(目标4)。

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).