deepTools: tools for exploring deep sequencing data

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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 (see Installation and The tools)
  • API – make use of your favorite deepTools modules in your own python programs (see deepTools API)

The flow chart below depicts the different tool modules that are currently available.

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If the file names in the figure mean nothing to you, please make sure to check our Glossary of NGS terms.

Contents:

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)

Tip

For support, questions, or feature requests contact: deeptools@googlegroups.com

Please cite deepTools2 as follows:

Ramírez, Fidel, Devon P. Ryan, Björn Grüning, Vivek Bhardwaj, Fabian Kilpert, Andreas S. Richter, Steffen Heyne, Friederike Dündar, and Thomas Manke. “deepTools2: a next generation web server for deep-sequencing data analysis.” Nucleic Acids Research (2016): gkw257.

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

deepTools Galaxy. code @ github.