deepTools: tools for exploring deep sequencing data¶
deepTools is 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.
There are 3 ways for using deepTools:
- Galaxy usage – our public deepTools Galaxy server let’s you use the deepTools within the familiar Galaxy framework without the need to master the command line
- command line usage – simply download and install the tools
- API – make use of your favorite deepTools modules in your own python programs
The flow chart below depicts the different tool modules that are currently available (deepTools modules are written in bold red and black font).
If the file names in the figure mean nothing to you, please make sure to check our Glossary of NGS terms.
While developing deepTools, we continuously strive to create software that fulfills the following criteria:
- efficiently extract reads from BAM files and perform various computations on them
- turn BAM files of aligned reads into bigWig files using different normalization strategies
- make use of multiple processors (speed!)
- generation of highly customizable images (change colours, size, labels, file format, etc.)
- enable customized down-stream analyses, meaning that every data set created can be stored by the user
- modular approach - compatibility, flexibility, scalability (i.e. we can add more and more modules and make use of established methods)
For support, questions, or feature requests contact: firstname.lastname@example.org
- Please cite deepTools as follows:
- Fidel Ramírez, Friederike Dündar, Sarah Diehl, Björn A. Grüning, and Thomas Manke. deepTools: a flexible platform for exploring deep-sequencing data. Nucl. Acids Res., 2014 doi:10.1093/nar/gku365
This tool suite is developed by the Bioinformatics Facility at the Max Planck Institute for Immunobiology and Epigenetics, Freiburg.