svist4get: a simple visualization tool for genomic tracks from sequencing experiments

BMC Bioinformatics. 2019 Mar 6;20(1):113. doi: 10.1186/s12859-019-2706-8.


Background: High-throughput sequencing often provides a foundation for experimental analyses in the life sciences. For many such methods, an intermediate layer of bioinformatics data analysis is the genomic signal track constructed by short read mapping to a particular genome assembly. There are many software tools to visualize genomic tracks in a web browser or with a stand-alone graphical user interface. However, there are only few command-line applications suitable for automated usage or production of publication-ready visualizations.

Results: Here we present svist4get, a command-line tool for customizable generation of publication-quality figures based on data from genomic signal tracks. Similarly to generic genome browser software, svist4get visualizes signal tracks at a given genomic location and is able to aggregate data from several tracks on a single plot along with the transcriptome annotation. The resulting plots can be saved as the vector or high-resolution bitmap images. We demonstrate practical use cases of svist4get for Ribo-Seq and RNA-Seq data.

Conclusions: svist4get is implemented in Python 3 and runs on Linux. The command-line interface of svist4get allows for easy integration into bioinformatics pipelines in a console environment. Extra customization is possible through configuration files and Python API. For convenience, svist4get is provided as pypi package. The source code is available at

Keywords: Genome browser; Genomic tracks; High-throughput sequencing; Next-generation sequencing; Python; RNA-Seq; Ribo-Seq; Visualization.

MeSH terms

  • Genome
  • Genomics / methods*
  • High-Throughput Nucleotide Sequencing / methods*
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • Ribosomes / metabolism
  • Software*


  • RNA, Messenger