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

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.

Researchers at Moscow State University 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. The researchers demonstrate practical use cases of svist4get for Ribo-Seq and RNA-Seq data.

Transcript-centric selection and visualization of a genomic window


The top track shows the YFL031W transcript structure with the collapsed intronic region (short red bar on the right). The tracks in the middle show Ribo-Seq (ribosome A-sites and aggregated read density) and RNA-Seq (aggregated read density) signals. The bottom track shows the 0, + 1, and + 2 reading frames with the start and stop codons marked by green and red bars, respectively. The transcript open reading frame is highlighted.

Availability – 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

Egorov AA, Sakharova EA, Anisimova AS, Dmitriev SE, Gladyshev VN, Kulakovskiy IV. (2019) svist4get: a simple visualization tool for genomic tracks from sequencing experiments. BMC Bioinformatics 20(1):113. [article]

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