Unknown

Dataset Information

0

Svist4get: a simple visualization tool for genomic tracks from sequencing experiments.


ABSTRACT: BACKGROUND: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. RESULTS: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. CONCLUSIONS: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/.

SUBMITTER: Egorov AA 

PROVIDER: S-EPMC6404320 | BioStudies | 2019-01-01

REPOSITORIES: biostudies

Similar Datasets

2018-01-01 | S-EPMC6343223 | BioStudies
2018-01-01 | S-EPMC6454532 | BioStudies
2020-01-01 | S-EPMC7291503 | BioStudies
1000-01-01 | S-EPMC2995121 | BioStudies
2018-01-01 | S-EPMC5753355 | BioStudies
2016-01-01 | S-EPMC4957989 | BioStudies
1000-01-01 | S-EPMC3596977 | BioStudies
2015-01-01 | S-EPMC4837986 | BioStudies
2011-01-01 | S-EPMC3232365 | BioStudies
2020-01-01 | S-EPMC7678096 | BioStudies