bactiviz: A Lightweight Command-Line Tool for Linear Collinearity Visualization of Bacterial Genomes

Abstract

Comparative visualization of bacterial genome structure is an important component of microbial genomics, enabling the inspection of genome conservation, rearrangements, inversions, insertions and deletions, and large-scale differences in gene organization. I present bactiviz, a lightweight command-line tool for generating linear collinearity maps of bacterial genomes. Implemented as a single-binary application in Rust, bactiviz uses MUMmer for nucleotide-level pairwise alignment and produces publication-ready, self-contained SVG figures. The tool is designed specifically for multi-replicon bacterial assemblies and supports chromosomes, plasmids, and other sequence records within GenBank and FASTA inputs. bactiviz provides optional origin normalization of circular replicons using a cascading gene-identification strategy based on gene symbols, locus tags, and product annotations, thereby accommodating heterogeneous real-world GenBank annotations. Conserved regions between adjacent genomes are represented as identity-scaled ribbons, including strand-aware visualization of inversions, while annotated genomic features are rendered as directional gene arrows. An automated label-placement procedure prioritizes user-specified genes and places additional labels where sufficient space is available, reducing overlap while retaining informative gene-level annotation at different output scales. A redundancy-resolution procedure further reduces visually cluttered alignments caused by repetitive sequences and duplicated genomic regions. The resulting SVG output is resolution-independent and can be directly incorporated into manuscripts or edited using standard vector-graphics software. bactiviz is intended for analyses in which a defined ordering of genomes is to be visualized rather than for all-against-all or multiple-genome alignment. By combining MUMmer-based alignment with native multi-replicon handling, genome-orientation normalization, exhaustive feature rendering, and automated annotation placement, bactiviz provides a lightweight and reproducible workflow for producing interpretable linear comparative-genomics figures.