LoVis4u: a locus visualization tool for comparative genomics and coverage profiles.

IF 4 Q1 GENETICS & HEREDITY
NAR Genomics and Bioinformatics Pub Date : 2025-02-24 eCollection Date: 2025-03-01 DOI:10.1093/nargab/lqaf009
Artyom A Egorov, Gemma C Atkinson
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引用次数: 0

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 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. The source code is available at the GitHub page: github.com/art-egorov/lovis4u. Detailed documentation that includes an example-driven guide is available from the software home page: art-egorov.github.io/lovis4u.

LoVis4u:用于比较基因组学和覆盖概况的基因座可视化工具。
比较基因组分析通常涉及基因组位点排列的可视化。虽然有几个软件工具可用于此任务,从Python和R库到独立的图形用户界面,但缺乏一种工具可以提供快速,自动化的使用和发布就绪的矢量图像的生成。在这里,我们介绍LoVis4u,一个命令行工具和Python API,设计用于高度可定制和快速可视化多个基因组位点。LoVis4u根据GenBank或GFF文件中的注释数据生成PDF格式的矢量图像。它能够可视化噬菌体的整个基因组以及质粒和更长的原核生物基因组的用户定义区域。此外,LoVis4u提供可选的数据处理步骤,以识别和突出输入序列中的辅助和核心基因。最后,LoVis4u支持测序实验中基因组信号轨迹谱的可视化。LoVis4u在Python3中实现,在Linux和MacOS上运行。命令行界面涵盖了大多数实际用例,而提供的Python API允许在Python程序中使用,集成到外部工具中,以及额外的定制。源代码可在GitHub页面:github.com/art-egorov/lovis4u。包含示例驱动指南的详细文档可从软件主页获得:art-egorov.github.io/lovis4u。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
CiteScore
8.00
自引率
2.20%
发文量
95
审稿时长
15 weeks
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