Biopipe: A Lightweight System Enabling Comparison of Bioinformatics Tools and Workflows

Analyzing next generation sequencing data always requires researchers to install many tools, prepare input data compliant to the required data format, and execute the tools in specific orders. Such tool installation and workflow execution process is tedious and error-prone, and becomes very challenging when researchers need to compare multiple alternative tool chains. To mitigate this problem, we developed a new lightweight and portable system, Biopipe, to simplify the creation and execution of bioinformatics tools and workflows, and to further enable the comparison between alternative tools or workflows. Biopipe allows users to create and edit workflows with user-friendly web interfaces, and automates tool installation as well as workflow synthesis by downloading and executing predefined Docker images. With Biopipe, biologists can easily experiment with and compare different bioinformatics tools and workflows without much computer science knowledge. There are mainly two parts in Biopipe: a web application and a standalone Java application. They are freely available at http://bench.cs.vt.edu:8282/Biopipe-Workflow-Editor-0.0.1/index.xhtml and https://code.vt.edu/saima5/Biopipe-Run-Workflow\n\nContactnm8247@cs.vt.edu\n\nSupplementary informationSupplementary data are available online.