Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis

Area of Science:

• Bioinformatics
• Computational Biology
• Genomics

Background:

• Quantitative transcriptome analysis is crucial for understanding gene expression.
• Existing tools often lack integration, customization, and robust quality assessment.
• The need for accessible, reproducible, and high-performance bioinformatics workflows is growing.

Purpose of the Study:

• To introduce Oqtans, an open-source workbench for quantitative transcriptome analysis within the Galaxy platform.
• To provide a modular and customizable pipeline architecture for comparative assessment of analysis tools and data quality.
• To integrate machine learning-powered tools that offer superior or equal performance to current state-of-the-art methods.

Main Methods:

• Development of Oqtans, an open-source workbench integrated into Galaxy.
• Implementation of a modular pipeline architecture supporting customizable computational workflows.
• Integration of machine learning-powered tools for short-read alignment, transcript identification/quantification, and differential expression analysis.
• Leveraging Galaxy's features for persistent storage, data exchange, and workflow documentation.

Main Results:

• Oqtans provides a complete transcriptome analysis workflow.
• Integrated machine learning tools demonstrate superior or equal performance compared to existing state-of-the-art tools.
• The workbench facilitates comparative assessment of tool and data quality through its modular design.
• Oqtans and Galaxy enable reproducible analysis with persistent storage and documentation.

Conclusions:

• Oqtans offers a powerful, flexible, and accessible platform for quantitative transcriptome analysis.
• Its integration with Galaxy and use of machine learning tools enhance analytical performance and reproducibility.
• The workbench aids in the interpretation of diverse experimental data through user-friendly use cases and extensibility.