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 t...

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Bibliographic Details
Published in:	BMC bioinformatics Vol. 20; no. 1; p. 113
Main Authors:	Egorov, Artyom A, Sakharova, Ekaterina A, Anisimova, Aleksandra S, Dmitriev, Sergey E, Gladyshev, Vadim N, Kulakovskiy, Ivan V
Format:	Journal Article
Language:	English
Published:	England BioMed Central Ltd 06-03-2019 BioMed Central BMC
Subjects:	Acids Analysis Annotations Bioinformatics Computational biology Computer graphics Computer programs Data analysis Data processing DNA sequencing Experiments Gene expression Gene mapping Genome Genomes Genomic tracks Genomics Genomics - methods Graphical user interface High-Throughput Nucleotide Sequencing - methods High-throughput sequencing Image resolution Life sciences Line interfaces Mapping Methods Molecular biology Next-generation sequencing Ribo-Seq Ribonucleic acid Ribosomes - metabolism RNA RNA sequencing RNA, Messenger - genetics RNA, Messenger - metabolism RNA-Seq Software Software development tools Source code Technology application Tracking User interface Visualization Visualization (Computer) Web browsers Russia Visualization Genome browser Next-generation sequencing High-throughput sequencing RNA-Seq Genomic tracks Ribo-Seq Python
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Summary:	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. 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. 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/.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	1471-2105 1471-2105
DOI:	10.1186/s12859-019-2706-8