Journal
BMC BIOINFORMATICS
Volume 20, Issue -, Pages -Publisher
BMC
DOI: 10.1186/s12859-019-2706-8
Keywords
Genomic tracks; Visualization; Next-generation sequencing; High-throughput sequencing; Ribo-Seq; RNA-Seq; Python; Genome browser
Categories
Funding
- Russian Federation [14.W03.31.0012]
- Russian Foundation for Basic Research [18-34-20024]
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BackgroundHigh-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.ResultsHere 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.Conclusionssvist4get 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/
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