index.rst

Welcome to pyGenomeTracks's documentation!

Standalone program and library to plot beautiful genome browser tracks

pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:

• bigwig
• bed/gtf (many options)
• bedgraph
• bedgraph matrices (like TAD-separation scores)
• epilogos
• narrow peaks
• links (represented as arcs, triangles or squares)
• Hi-C matrices (as triangle or squares)
• fasta
• maf (multiple alignment format)

Here is a scheme which describe how pyGenomeTracks is working (graphical abstract of Lopez-Delisle et al. 2020):

pyGenomeTracks can make plots with or without Hi-C data. The following is an example output of pyGenomeTracks from Ramírez et al. 2017.

There are 3 ways for using pyGenomeTracks:

• Galaxy usage -- the public European Galaxy server let's you use pyGenomeTracks within the familiar Galaxy framework without the need to master the command line
• command line usage -- simply download and install the tool (see :doc:`content/installation` and :doc:`content/usage`)

Table of content

.. toctree::
   :maxdepth: 1
   :caption: Contents:

   content/installation
   content/usage
   content/citation
   content/all_tracks
   content/examples
   content/possible-parameters
   content/adding-new-tracks
   content/releases
   content/faq