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

• DOI: 10.1371/journal.pcbi.1010998
• Publication Date: 2023-04-04T18:03:47Z
• Authors: Andrés Cumsille; Roberto E. Durán; Andrea Rodríguez-...; Vicente Saona-Urm...; Beatriz Cámara; Michael Seeger; Mauricio Araya; Nicolás Jara; Carlos Buil-Aranda
• Keywords: Genome, Microbial; Bacteria; QH301-705.5; Genomics; Biology (General); Archaea; Software; Research Article

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