Tools to process and analyze deep sequencing data.
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User-friendly tools for exploring deep-sequencing data

deepTools addresses the challenge of handling the large amounts of data that are now routinely generated from DNA sequencing centers. 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.

For support, questions, or feature requests contact:


Ramírez F, Ryan DP, Grüning B, Bhardwaj V, Kilpert F, Richter AS, Heyne S, Dündar F, Manke T. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Research. 2016 Apr 13:gkw257.


Our documentation contains more details on the individual tool scopes and usages and an introduction to our deepTools Galaxy web server including step-by-step protocols.

Please see also the FAQ, which we update regularly. Our Gallery may give you some more ideas about the scope of deepTools.

For more specific troubleshooting, feedback, and tool suggestions, contact us via


deepTools are available for:

  • Command line usage (via pip/anaconda/github)
  • Integration into Galaxy servers (via toolshed/API/web-browser)

There are many easy ways to install deepTools. Details can be found here

Install by cloning this repository:

You can install any one of the deepTools branches on command line (linux/mac) by cloning this git repository :

$ git clone
$ cd deepTools
$ python install

By default, the script will install the python library and executable codes globally, which means you need to be root or administrator of the machine to complete the installation. If you need to provide a nonstandard install prefix, or any other nonstandard options, you can provide many command line options to the install script.

$ python --help

For example, to install under a specific location use:

$ python install --prefix <target directory>

To install into your home directory, use:

$ python install --user

Galaxy Installation

deepTools can be easily integrated into Galaxy. Please see the installation instructions in our documentation for further details.

Note: From version 2.3 onwards, deepTools support python3. In case of any problems running with python3/python2, contact our user group :

This tool suite is developed by the Bioinformatics Facility at the Max Planck Institute for Immunobiology and Epigenetics, Freiburg.

Documentation | deepTools Galaxy | FAQ