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pygenometracks website  

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)

Environment Modules

Run module spider pygenometracks to find out what environment modules are available for this application.

System Variables

  • HPC_PYGENOMETRACKS_DIR - installation directory
  • HPC_PYGENOMETRACKS_BIN - executable directory


If you publish research that uses pygenometracks you have to cite it as follows:

If you use pyGenomeTracks in your analysis, you can cite the following papers:

Fidel Ramírez, Vivek Bhardwaj, Laura Arrigoni, Kin Chung Lam, Björn A. Grüning, José Villaveces, Bianca Habermann, Asifa Akhtar & Thomas Manke. High-resolution TADs reveal DNA sequences underlying genome organization in flies. Nature Communications (2018) doi:10.1038/s41467-017-02525-w

Lopez-Delisle L, Rabbani L, Wolff J, Bhardwaj V, Backofen R, Grüning B, Ramírez F, Manke T. pyGenomeTracks: reproducible plots for multivariate genomic data sets. Bioinformatics. 2020 Aug 3:btaa692. doi: 10.1093/bioinformatics/btaa692. Epub ahead of print. PMID: 32745185.