SnakeBITE: A SNAKEmake-Based Interface for Third-Generation Sequencing Data Analysis

In recent years, the use of computational pipelines for the analysis of omic data has become routine in bioinformatics, particularly with the advent of Next-Generation Sequencing (NGS) technologies. These technologies generate vast amounts of data that necessitate sophisticated analysis methods, often requiring programming skills and command-line interface proficiency. This complexity poses challenges for users from various backgrounds, including clinicians and biologists. Current solutions often involve workflow management tools and graphical user interfaces to simplify pipeline creation and execution. However, these tools predominantly cater to NGS data and are not fully adaptable to Third-Generation Sequencing (TGS) data, such as that produced by Oxford Nanopore Technologies (ONT). Here we present SnakeBITE, a modular genomic data analysis pipeline builder based on the Snakemake workflow manager, integrated with an interactive Shiny-based interface. SnakeBITE enables users to configure and execute TGS data analysis workflows locally without requiring programming expertise. The application supports the full ONT genomics data analysis pipeline, including base calling, alignment, variant calling, and annotation. Our results demonstrate SnakeBITE's capacity to handle various stages of ONT data analysis efficiently, offering a user-friendly and highly customizable tool that bridges the gap between sophisticated data analysis and user accessibility.