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deepTools

  • Description

    a suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq. deepTools contains useful modules to process the mapped reads data for multiple quality checks, creating normalized coverage files in standard bedGraph and bigWig file formats, that allow comparison between different files (for example, treatment and control). Finally, using such normalized and standardized files, deepTools can create many publication-ready visualizations to identify enrichments and for functional annotations of the genome.

  • Usage

    To list all executables provided by deepTools, run: $ sbgrid-list deeptools Copy to clipboard

  • Installation

    Use the following command to install this title with the CLI client: $ sbgrid-cli install deeptools Copy to clipboard Available operating systems: Linux 64, OS X INTEL

  • Primary Citation*

    F. Ramírez, D. P. Ryan, B. Grüning, V. Bhardwaj, F. Kilpert, A. S. Richter, S. Heyne, F. Dündar, and T. Manke. 2016. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Research. 44(1): W160-W165.
    (Note: Web Server issue)


    • *Full citation information available through

  • Keywords

    High-throughput sequencing

  • Default Versions

    Linux 64:  3.5.4 (461.8 MB)
    OS X INTEL:  3.5.4 (439.3 MB)

  • Other Versions

      Linux 64:

      3.3.1 (1.1 GB) , 3.5.1 (490.1 MB) , 3.5.2 (457.7 MB) , 3.5.3 (461.8 MB)

    • OS X INTEL:

      3.3.1 (438.9 MB) , 3.5.1 (444.3 MB) , 3.5.2 (435.1 MB) , 3.5.3 (439.0 MB)

  • Developers

    Thomas Manke, Devon Ryan, Fidel Ramírez

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