Pygenometracks
Description
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
Citation
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.