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

Abstract

The increase in microbial sequenced genomes from pure cultures and metagenomic samples reflects the current attainability of whole-genome and shotgun sequencing methods. However, software for genome visualization still lacks automation, integration of different analyses, and customizable options for non-experienced users. In this study, we introduce GenoVi, a Python command-line tool able to create custom circular genome representations for the analysis and visualization of microbial genomes and sequence elements. It is designed to work with complete or draft genomes, featuring customizable options including 25 different built-in color palettes (including 5 color-blind safe palettes), text formatting options, and automatic scaling for complete genomes or sequence elements with more than one replicon/sequence. Using a Genbank format file as the input file or multiple files within a directory, GenoVi (i) visualizes genomic features from the GenBank annotation file, (ii) integrates a Cluster of Orthologs Group (COG) categories analysis using DeepNOG, (iii) automatically scales the visualization of each replicon of complete genomes or multiple sequence elements, (iv) and generates COG histograms, COG frequency heatmaps and output tables including general stats of each replicon or contig processed. GenoVi’s potential was assessed by analyzing single and multiple genomes of Bacteria and Archaea. Paraburkholderia genomes were analyzed to obtain a fast classification of replicons in large multipartite genomes. GenoVi works as an easy-to-use command-line tool and provides customizable options to automatically generate genomic maps for scientific publications, educational resources, and outreach activities. GenoVi is freely available and can be downloaded from https://github.com/robotoD/GenoVi.

Analysis of global Aeromonas caviae genomes revealed that strains carrying T6SS are more common in human gastroenteritis than in environmental sources and are often phylogenetically related

“…Statistics of the reads were generated using NanoStat (v 1.5.0), and genome coverage was estimated using Minimap2 (v 2.17) and qualimap (v 2.1.11) [11, 16, 17]. A circular representation of the A20-9 plasmid was generated using GenoVi [18]. Plasmid similarity was searched against the NCBI database using blast n. Plasmids with at least 90 % query coverage from completely sequenced genomes were determined as similar.…”

Genomic and vaccine preclinical studies reveal a novel mouse-adapted Helicobacter pylori model for the hpEastAsia genotype in Southeast Asia

“…Virulence gene composition was identified using the chromosomal data of strain HP26695 (GenBank accession number NC000915). The circular map of the studied strains was illustrated using the GenoVi software [28]. In order to locate changes in amino acid composition associated with AMR, substitution data of AMR-related genes in H. pylori strains were referenced according to AMR patterns and genetic elements from Shanghai [29].…”