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):

_images/graphicalabstract.png

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

_images/hic_example_nat_comm_small.png

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 Installation and Usage)

Table of content

Contents: