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

BMC Bioinformatics

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[1] 0000 0001 2192 9124, grid.4886.2, Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina 3, 119991, Moscow, Russia;0000 0001 2342 9668, grid.14476.30, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskiye gory 1, 119234, Moscow, Russia;0000 0001 2192 9124, grid.4886.2, Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina 3, 119991, Moscow, Russia;0000 0001 2192 9124, grid.4886.2, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, 119991, Moscow, Russia;0000 0004 0638 149X, grid.435288.0, Institute of Mathematical Problems of Biology RAS - the Branch of Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, Vitkevicha 1, 142290, Pushchino, Moscow Region, Russia;0000 0001 2342 9668, grid.14476.30, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskiye gory 1, 119234, Moscow, Russia;0000 0001 2342 9668, grid.14476.30, Department of Medical Physics, Faculty of Physics, Lomonosov Moscow State University, Leninskiye gory 1-2, 119991, Moscow, Russia;0000 0001 2342 9668, grid.14476.30, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskiye gory 1, 119234, Moscow, Russia;0000 0001 2342 9668, grid.14476.30, Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskiye gory 1-73, 119234, Moscow, Russia;0000 0001 2342 9668, grid.14476.30, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskiye gory 1, 119234, Moscow, Russia;0000 0001 2342 9668, grid.14476.30, Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskiye gory 1-73, 119234, Moscow, Russia;0000 0001 2192 9124, grid.4886.2, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, 119991, Moscow, Russia;0000 0001 2342 9668, grid.14476.30, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskiye gory 1, 119234, Moscow, Russia;0000 0004 0378 8294, grid.62560.37, Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, 02115, Boston, MA, USA;

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

DOI  :  10.1186/s12859-019-2706-8

来源: publisher

【 摘 要 】

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/

【 授权许可】

CC BY