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Updated: Jan 17, 2026
05:07
Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes
Published on: November 7, 2025
351
Robust software development practices improve citations of RNA-seq tools
Biorxiv : the Preprint Server for Biology
|September 18, 2025
Summary
Rigorous software development practices are crucial for RNA sequencing (RNA-seq) tools. Studies show that well-developed RNA-seq software is more widely adopted and cited in scientific research.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- RNA sequencing (RNA-seq) is vital for transcriptomic analysis in biology and medicine.
- The increasing number of RNA-seq tools requires robust development and distribution practices.
- Ensuring software reliability, transparency, and reproducibility is essential for scientific trust.
Purpose of the Study:
- To assess the development, maintenance, and distribution of RNA-seq tools.
- To identify factors influencing the adoption and dependability of RNA-seq software.
- To establish a link between software development practices and tool adoption.
Main Methods:
- A comprehensive assessment of 434 RNA-seq tools developed between 2008 and 2024.
- Categorization of tools based on analysis type.
- Evaluation of development methodologies, distribution, and adoption attributes (e.g., package managers, containerization, documentation).
Main Results:
- A significant positive association was found between rigorous software development practices and RNA-seq tool adoption, measured by citations (p < 2.2e-16).
- Key characteristics contributing to widespread adoption include package manager availability, containerization, multithreading, documentation quality, and example datasets.
- The study provides the first documented evidence linking software quality to tool usage in the RNA-seq field.
Conclusions:
- Rigorous software development practices are strongly correlated with the adoption and impact of RNA-seq tools.
- Identifying characteristics of successful software can guide the development of more robust and user-friendly tools.
- The findings support the need for community-wide standards in RNA-seq software development to enhance reliability and reproducibility.
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