LoVis4u : a locus visualization tool for comparative genomics and coverage profiles
Egorov, Artyom A. LU
and Atkinson, Gemma C.
LU
(2025)
In NAR Genomics and Bioinformatics
7(1).
- Abstract
Comparative genomic analysis often involves visualization of alignments of genomic loci. While several software tools are available for this task, ranging from Python and R libraries to stand-alone graphical user interfaces, a tool is lacking that offers fast, automated usage and the production of publication-ready vector images. Here we present LoVis4u, a command-line tool and Python API designed for highly customizable and fast visualization of multiple genomic loci. LoVis4u generates vector images in PDF format based on annotation data from GenBank or GFF files. It is capable of visualizing entire genomes of bacteriophages as well as plasmids and user-defined regions of longer prokaryotic genomes. Additionally, LoVis4u offers... (More)
Comparative genomic analysis often involves visualization of alignments of genomic loci. While several software tools are available for this task, ranging from Python and R libraries to stand-alone graphical user interfaces, a tool is lacking that offers fast, automated usage and the production of publication-ready vector images. Here we present LoVis4u, a command-line tool and Python API designed for highly customizable and fast visualization of multiple genomic loci. LoVis4u generates vector images in PDF format based on annotation data from GenBank or GFF files. It is capable of visualizing entire genomes of bacteriophages as well as plasmids and user-defined regions of longer prokaryotic genomes. Additionally, LoVis4u offers optional data processing steps to identify and highlight accessory and core genes in input sequences. Finally, LoVis4u supports the visualization of genomic signal track profiles from sequencing experiments. LoVis4u is implemented in Python3 and runs on Linux and MacOS. The command-line interface covers most practical use cases, while the provided Python API allows usage within a Python program, integration into external tools, and additional customization.
(Less)
- author
- Egorov, Artyom A.
LU
and Atkinson, Gemma C.
LU
- organization
- publishing date
- 2025-03
- type
- Contribution to journal
- publication status
- published
- subject
- in
- NAR Genomics and Bioinformatics
- volume
- 7
- issue
- 1
- article number
- lqaf009
- publisher
- Oxford University Press
- external identifiers
-
- scopus:85218957339
- pmid:40007724
- ISSN
- 2631-9268
- DOI
- 10.1093/nargab/lqaf009
- language
- English
- LU publication?
- yes
- id
- bbc082c9-5040-4266-bd39-2e1414b13f22
- date added to LUP
- 2025-06-19 10:33:14
- date last changed
- 2025-07-17 13:38:42
@article{bbc082c9-5040-4266-bd39-2e1414b13f22,
abstract = {{<p>Comparative genomic analysis often involves visualization of alignments of genomic loci. While several software tools are available for this task, ranging from Python and R libraries to stand-alone graphical user interfaces, a tool is lacking that offers fast, automated usage and the production of publication-ready vector images. Here we present LoVis4u, a command-line tool and Python API designed for highly customizable and fast visualization of multiple genomic loci. LoVis4u generates vector images in PDF format based on annotation data from GenBank or GFF files. It is capable of visualizing entire genomes of bacteriophages as well as plasmids and user-defined regions of longer prokaryotic genomes. Additionally, LoVis4u offers optional data processing steps to identify and highlight accessory and core genes in input sequences. Finally, LoVis4u supports the visualization of genomic signal track profiles from sequencing experiments. LoVis4u is implemented in Python3 and runs on Linux and MacOS. The command-line interface covers most practical use cases, while the provided Python API allows usage within a Python program, integration into external tools, and additional customization.</p>}},
author = {{Egorov, Artyom A. and Atkinson, Gemma C.}},
issn = {{2631-9268}},
language = {{eng}},
number = {{1}},
publisher = {{Oxford University Press}},
series = {{NAR Genomics and Bioinformatics}},
title = {{LoVis4u : a locus visualization tool for comparative genomics and coverage profiles}},
url = {{http://dx.doi.org/10.1093/nargab/lqaf009}},
doi = {{10.1093/nargab/lqaf009}},
volume = {{7}},
year = {{2025}},
}