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

Andrea Bimbocci1, Marta Baragli1, Alberto Magi1

  • 1Department of Information Engineering, University of Florence, 50139 Florence, Italy.

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|February 27, 2026
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Summary
This summary is machine-generated.

SnakeBITE simplifies Third-Generation Sequencing (TGS) data analysis for researchers. This user-friendly tool enables local execution of Oxford Nanopore Technologies (ONT) genomic pipelines without coding, enhancing accessibility.

Keywords:
genomicsgraphical user interfacenanopore sequencing

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Area of Science:

  • Bioinformatics and Computational Biology
  • Genomics and Omics Data Analysis
  • Bioinformatics Tool Development

Background:

  • Computational pipelines are essential for analyzing omics data, especially from Next-Generation Sequencing (NGS).
  • Analyzing Third-Generation Sequencing (TGS) data, like Oxford Nanopore Technologies (ONT), presents unique challenges due to its complexity.
  • Existing tools often focus on NGS data and lack adaptability for TGS, creating a barrier for non-programmers.

Purpose of the Study:

  • To develop a user-friendly, modular pipeline builder for Third-Generation Sequencing (TGS) genomic data analysis.
  • To enable researchers, including clinicians and biologists, to execute TGS workflows locally without programming expertise.
  • To provide a customizable solution for the full Oxford Nanopore Technologies (ONT) data analysis pipeline.

Main Methods:

  • Development of SnakeBITE, a pipeline builder based on the Snakemake workflow manager.
  • Integration of an interactive Shiny-based graphical user interface (GUI).
  • Implementation of support for the complete ONT genomics data analysis workflow: base calling, alignment, variant calling, and annotation.

Main Results:

  • SnakeBITE successfully enables local configuration and execution of TGS data analysis workflows.
  • The tool efficiently handles various stages of ONT data analysis, from base calling to annotation.
  • Demonstrated user-friendliness and high customizability for TGS data analysis.

Conclusions:

  • SnakeBITE provides an accessible and efficient solution for Third-Generation Sequencing (TGS) data analysis.
  • The tool bridges the gap between complex genomic data analysis and user accessibility for researchers.
  • SnakeBITE empowers users without programming expertise to perform comprehensive ONT data analysis.