deepTools4: Faster, Scalable, and Modernized Genomic Data Analysis

Deboutte, W.; Salatino, A.; Maier, W.; Videm, P.; Navandar, M.; Erikson, G.; Momin, S.; Caballero-Perez, J.; Rabbani, L.; Lopez-Delisle, L.; Grüning, B.; Manke, T.

doi:10.64898/2026.11.11.765524

bioRxiv · 10.64898/2026.11.11.765524

deepTools4: Faster, Scalable, and Modernized Genomic Data Analysis

Deboutte, W.·Salatino, A.·Maier, W.·Videm, P.·Navandar, M.·Erikson, G.·Momin, S.·Caballero-Perez, J.·Rabbani, L.·Lopez-Delisle, L.·Grüning, B.·Manke, T.

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Abstract

The deepTools suite is widely used for quality control, summarization, and visualization of high-throughput sequencing data. However, as genomic datasets grow in scale and depth, existing tools often become computational bottlenecks. We present deepTools4, a modernized framework designed for high performance, scalability, and enhanced usability, while maintaining seamless integration with the Galaxy platform. Core functionality has been rewritten and thoroughly benchmarked, achieving substantial computational speed-ups. Visualization tools have been modernized to provide more intuitive, high-quality graphical outputs. In addition, our testing framework has been expanded to facilitate continuous development and ensure robustness. We demonstrate the utility of deepTools4 across diverse epigenomics and transcriptomics datasets, highlighting its ability to summarize genome-wide signals, apply a wide range of common normalization methods, and visualize enrichment patterns. The enhanced deepTools4 framework delivers a faster, more scalable solution for reproducible genome-wide analysis and interpretation across many sequencing modalities. Availability: https://github.com/deeptools/deepTools/

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Deboutte, W., Salatino, A., Maier, W., Videm, P., Navandar, M., Erikson, G., Momin, S., Caballero-Perez, J., Rabbani, L., Lopez-Delisle, L., Grüning, B., Manke, T.. 2026-11-13. deepTools4: Faster, Scalable, and Modernized Genomic Data Analysis. https://doi.org/10.64898/2026.11.11.765524

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