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

rna-seq

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 https://bitbucket.org/artegorov/svist4get/.

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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