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Svist4get : A simple visualization tool for genomic tracks from sequencing experiments

Egorov, Artyom A. LU orcid ; Sakharova, Ekaterina A. ; Anisimova, Aleksandra S. ; Dmitriev, Sergey E. ; Gladyshev, Vadim N. and Kulakovskiy, Ivan V. (2019) In BMC Bioinformatics 20. p.1-6
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,... (More)

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/

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author
; ; ; ; and
publishing date
type
Contribution to journal
publication status
published
keywords
Genome browser, Genomic tracks, High-throughput sequencing, Next-generation sequencing, Python, Ribo-Seq, RNA-Seq, Visualization
in
BMC Bioinformatics
volume
20
article number
113
pages
1 - 6
publisher
BioMed Central (BMC)
external identifiers
  • pmid:30841857
  • scopus:85062500730
ISSN
1471-2105
DOI
10.1186/s12859-019-2706-8
language
English
LU publication?
no
additional info
Publisher Copyright: © 2019 The Author(s).
id
00437574-9a1e-4ef8-ad63-0a5a22980444
date added to LUP
2022-08-24 23:16:29
date last changed
2025-03-18 09:46:28
@article{00437574-9a1e-4ef8-ad63-0a5a22980444,
  abstract     = {{<p>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/</p>}},
  author       = {{Egorov, Artyom A. and Sakharova, Ekaterina A. and Anisimova, Aleksandra S. and Dmitriev, Sergey E. and Gladyshev, Vadim N. and Kulakovskiy, Ivan V.}},
  issn         = {{1471-2105}},
  keywords     = {{Genome browser; Genomic tracks; High-throughput sequencing; Next-generation sequencing; Python; Ribo-Seq; RNA-Seq; Visualization}},
  language     = {{eng}},
  month        = {{03}},
  pages        = {{1--6}},
  publisher    = {{BioMed Central (BMC)}},
  series       = {{BMC Bioinformatics}},
  title        = {{Svist4get : A simple visualization tool for genomic tracks from sequencing experiments}},
  url          = {{http://dx.doi.org/10.1186/s12859-019-2706-8}},
  doi          = {{10.1186/s12859-019-2706-8}},
  volume       = {{20}},
  year         = {{2019}},
}