seabreeze

seabreeze is a tool for comprehensively analyzing genetic variation among bacterial genomes caused by structural mutations. It manages a workflow that combines existing packages and custom scripts to automate and unite several analyses into a single, easy-to-use pipeline. For specified pairs of bacterial genomes, it can:

• Compute size difference between genomes
• Predict the location of insertion sequences
• Predict structural mutations (inversions, deletions, translocations, duplications)
• Generate intuitive synteny plots to visualise structural variation
• Analyse the effect of structural mutations on the balance of the two replichores
• Predict the putative mechanism of inversions and deletions
• Annotate the genes contained in the mutated regions

Please refer to the official documentation for information on installation and usage.

If you use seabreeze, please cite

Zibbu et al., (2025). seabreeze: A Pipeline for Analyzing Structural Variation Between Bacterial Genome Assemblies. Journal of Open Source Software, 10(111), 8065, https://doi.org/10.21105/joss.08065

seabreeze was developed at the Barrick Lab at the University of Texas at Austin.

Have a question, issue to report, feature to request or code to contribute? Please see the contributions.