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hDNApipe: streamlining human genome analysis and interpretation with an intuitive and user-friendly interface.

Yaxin Zhang¹, Qiqin Wu², Ying Zhou¹

¹Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, PR China.

NAR Genomics and Bioinformatics

|June 27, 2025

Summary

hDNApipe is a new, user-friendly tool for human genome analysis, simplifying complex next-generation sequencing data interpretation. It offers efficient variant analysis and visualization, improving genomic research workflows.

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Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Next-generation sequencing (NGS) has led to numerous human genome analysis tools, creating pipeline complexity.
A need exists for efficient, user-friendly pipelines to streamline genomic data analysis and interpretation.

Purpose of the Study:

Introduce hDNApipe, a flexible, end-to-end pipeline for human genomic data analysis.
Provide a tool with both command-line and graphical user interfaces for customized analysis.
Simplify the installation and dependency management of genomic analysis tools.

Main Methods:

Developed using bash scripts and Python's Tkinter GUI library.
Features dual-mode operation (CLI and GUI) with customizable parameters.
Includes a Docker setup for simplified installation and dependency management.

Main Results:

hDNApipe facilitates direct acquisition of variants and associated information.
Optional visualization of variants and downstream analysis capabilities are included.
Benchmarking demonstrated superior performance in time consumption, precision, and sensitivity compared to other pipelines.

Conclusions:

hDNApipe offers an efficient, user-friendly solution for human genomic data analysis.
Its flexibility, dual-mode operation, and simplified installation enhance usability for researchers.
The tool shows outstanding performance, making it a valuable asset for genomic research workflows.