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 bug reports and feature requests please open an issue on github.
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. deepTools4: Faster, Scalable, and Modernized Genomic Data Analysis. bioRxiv. 2026 Nov 13. doi:10.64898/2026.11.11.765524
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. NAR. 2016 Apr 13. doi:10.1093/nar/gkw257
Our documentation contains more details on the individual tool scopes and usages and an introduction to using deepTools in Galaxy 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.
deepTools is available for:
- Command line usage (via pip / conda / github)
- Integration into Galaxy servers (via toolshed/API/web-browser)
There are many ways to install deepTools. More details can be found here.
In Brief, to install stable released version:
Install via pip
$ pip install deeptools
Install via conda
$ conda install -c conda-forge -c bioconda deeptools
Install via uv / pipx / pixi
$ uv tool install deeptools
$ pipx install deeptools
$ pixi global install -c conda-forge -c bioconda deeptools
You can also install the latest development version (if you want to contribute or have the latest features). The easiest way to do this is clone the repository and install with pixi (which will take care of the system dependencies via conda for you):
Install by cloning the repository
$ git clone https://github.com/deeptools/deepTools
$ cd deepTools
$ pixi install
pixi install pins the whole build toolchain (Rust, maturin, libclang, HTSlib, ...) via
conda -- see pyproject.toml's [tool.pixi.dependencies] for exactly what's
pinned. Building without pixi (via uv / pip / pipx) is possible too, but then you're responsible
for providing that same toolchain yourself; see the "Building from
source"
section of the docs.
deepTools can be easily integrated into Galaxy. Please see the installation instructions in our documentation for further details.