deepTools2 is an updated web server for deep-sequencing data analysis, built on the Galaxy platform. It offers a range of tools for quality control, data processing, normalization, integration, and visualization. The server is freely available at deeptools.ie-freiburg.mpg.de and can be deployed via the Galaxy toolshed. It supports various file formats, including BAM, bigWig, and BED, and provides customizable visualizations and publication-ready outputs. The server also includes a public API for accessing its functionality. Key enhancements in deepTools2 include improved quality control tools such as plotCoverage and plotPCA, which help assess sequencing depth and sample variability. The tool also supports the analysis of multiple samples and the visualization of correlation structures. Additionally, deepTools2 can process new sequencing read types, including spliced reads and MNase-seq data, and has significantly improved processing speed for bigWig files using the pyBigWig and libBigWig libraries. The server also offers enhanced processing flexibility, allowing for combined filtering, normalization, and format conversion in a single framework. It supports a wide range of downstream analyses, including clustering and visualization of genomic data. The new tools multiBamSummary and multiBigwigSummary allow for the summarization of data from multiple samples into a single score per region. The computeMatrix tool is now capable of aggregating regional scores from multiple samples into a single matrix for visualization. The deepTools2 web server is implemented within the Galaxy framework and is accessible via Docker, allowing for easy deployment on local machines. It is also available as a Python package, enabling integration into other programs. The server provides extensive documentation, testing, and community support, with continuous updates and improvements. The modular design of deepTools2 allows for the addition of new functionalities and is well-suited for handling large-scale data production and single-cell sequencing. The server is a versatile platform for training workshops and data sharing among collaborators.deepTools2 is an updated web server for deep-sequencing data analysis, built on the Galaxy platform. It offers a range of tools for quality control, data processing, normalization, integration, and visualization. The server is freely available at deeptools.ie-freiburg.mpg.de and can be deployed via the Galaxy toolshed. It supports various file formats, including BAM, bigWig, and BED, and provides customizable visualizations and publication-ready outputs. The server also includes a public API for accessing its functionality. Key enhancements in deepTools2 include improved quality control tools such as plotCoverage and plotPCA, which help assess sequencing depth and sample variability. The tool also supports the analysis of multiple samples and the visualization of correlation structures. Additionally, deepTools2 can process new sequencing read types, including spliced reads and MNase-seq data, and has significantly improved processing speed for bigWig files using the pyBigWig and libBigWig libraries. The server also offers enhanced processing flexibility, allowing for combined filtering, normalization, and format conversion in a single framework. It supports a wide range of downstream analyses, including clustering and visualization of genomic data. The new tools multiBamSummary and multiBigwigSummary allow for the summarization of data from multiple samples into a single score per region. The computeMatrix tool is now capable of aggregating regional scores from multiple samples into a single matrix for visualization. The deepTools2 web server is implemented within the Galaxy framework and is accessible via Docker, allowing for easy deployment on local machines. It is also available as a Python package, enabling integration into other programs. The server provides extensive documentation, testing, and community support, with continuous updates and improvements. The modular design of deepTools2 allows for the addition of new functionalities and is well-suited for handling large-scale data production and single-cell sequencing. The server is a versatile platform for training workshops and data sharing among collaborators.