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deepTools
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User-friendly tools for exploring deep-sequencing data
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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 or questions please make a post on `Biostars <http://biostars.org>`__. For feature requests, please open an issue on `github <http://github.com/deeptools/deeptools>`__.

For further documentation, please see our `read the docs page <http://deeptools.readthedocs.org/>`__.

Citation:
^^^^^^^^^

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. <https://nar.oxfordjournals.org/content/early/2016/04/12/nar.gkw257.abstract>`__
Nucleic Acids Research. 2016 Apr 13:gkw257.
