GenoVi, an open-source automated circular genome visualizer for bacteria and archaea

Area of Science:

• Genomics
• Bioinformatics
• Microbial Ecology

Background:

• Advances in whole-genome and shotgun sequencing have increased microbial genome data availability.
• Current genome visualization software often lacks automation, integration, and user-friendly customization for non-experts.
• Efficient visualization tools are crucial for analyzing complex microbial genomes.

Purpose of the Study:

• To introduce GenoVi, a novel Python command-line tool for custom circular microbial genome visualization.
• To provide automated analysis and customizable features for diverse user needs.
• To facilitate the interpretation of microbial genomes and sequence elements.

Main Methods:

• GenoVi accepts GenBank format files or directories of files as input.
• It visualizes genomic features, integrates Cluster of Orthologs Group (COG) analysis via DeepNOG, and automatically scales visualizations.
• The tool generates COG histograms, heatmaps, and statistical tables for replicons or contigs.

Main Results:

• GenoVi successfully generated custom circular genome maps for various Bacteria and Archaea.
• Analysis of Paraburkholderia genomes demonstrated efficient classification of replicons in multipartite genomes.
• The tool provides customizable options, including 25 color palettes (5 color-blind safe) and text formatting.

Conclusions:

• GenoVi is an easy-to-use, command-line tool for automated and customizable microbial genome visualization.
• It enhances the analysis and presentation of genomic data for scientific publications, education, and outreach.
• GenoVi is freely available, promoting broader accessibility in bioinformatics research.