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.