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DROMPAplus: a pipeline tool for ChIP-seq analysis
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DROMPA (DRaw and Observe Multiple enrichment Profiles and Annotation) is a ChIP-seq pipeline tool that meets various needs, including quality check, analysis, and visualization of multiple ChIP samples.

DROMPAplus is an update of `DROMPA3 <https://github.com/rnakato/DROMPA3>`_. It is written in C++ and runs from a single launch command on conventional Linux systems.

* The main features of DROMPAplus are summarized below. DROMPAplus:

    * Accepts multiple map file formats (SAM, BAM, CRAM, Bowtie, TagAlign(.gz)) and read distribution formats (WIG(.gz), bigWig, bedGraph).
    * Supports spike-in normalization and total read normalization.
    * Outputs various quality metrics for ChIP-seq analysis.
    * Visualizes read distributions in conventional PDF format; therefore, no additional programs are required which is preferable for many users, especially when sharing results (e.g., on cloud storage) with collaborators who do not have a strong bioinformatics background.
    * Automatically estimates the fragment length from single-end reads using `SSP <https://github.com/rnakato/SSP>`_.
    * Can visualize two samples in a single line, which delineates the co-occurrence (e.g., H3K4me3 and H3K27ac) and exclusivity (e.g., H3K27me3 and H3K36me3) of read enrichment. Transparency (alpha) of read color can be specified.
    * Supports chromatin loops from ChIA-PET (Mango format) and Hi-C (HICCUPS format) with colors corresponding to the p-values.
    * Bases the HEATMAP command on Python3, which enables flexible customization.

.. figure:: img/workflow.jpg
   :width: 600px
   :align: center
   :alt: Alternate

   Schematic representation of DROMPA+ features and functionality.

Contents:
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.. toctree::
   :numbered:
   :glob:
   :maxdepth: 2

   content/Install
   content/parse2wig
   content/drompa
   content/Appendix


Citation:
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* Nakato R., Sakata T., Methods for ChIP-seq analysis: A practical workflow and advanced applications, *Methods*, 2020.

Contact:
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:Mail: rnakato AT iqb.u-tokyo.ac.jp
:Twitter: @RyuichiroNakato