https://github.com/barricklab/seabreeze

seabreeze: A Pipeline for Analyzing Structural Variation Between Bacterial Genome Assemblies
https://github.com/barricklab/seabreeze

bioinformatics-pipeline experimental-evolution long-read-sequencing structural-variation

Last synced: 2 months ago
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seabreeze: A Pipeline for Analyzing Structural Variation Between Bacterial Genome Assemblies

• Host: GitHub
• URL: https://github.com/barricklab/seabreeze
• Owner: barricklab
• License: mit
• Created: 2024-08-28T17:42:04.000Z (almost 2 years ago)
• Default Branch: main
• Last Pushed: 2025-09-18T14:47:14.000Z (9 months ago)
• Last Synced: 2026-01-26T16:16:46.272Z (5 months ago)
• Topics: bioinformatics-pipeline, experimental-evolution, long-read-sequencing, structural-variation
• Language: Python
• Homepage: https://barricklab.github.io/seabreeze/
• Size: 20 MB
• Stars: 4
• Watchers: 1
• Forks: 2
• Open Issues: 7
• Metadata Files:
  • Readme: README.md
  • Contributing: contributing.md
  • License: LICENSE
  • Citation: CITATION.cff

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README

          
# seabreeze

![workflow](https://github.com/barricklab/seabreeze/actions/workflows/ci.yaml/badge.svg)

[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)

[![Latest release](https://badgen.net/github/release/Naereen/Strapdown.js)](https://github.com/barricklab/seabreeze/releases)

[![Anaconda-Server Badge](https://anaconda.org/bioconda/seabreeze-genomics/badges/platforms.svg)](https://anaconda.org/bioconda/seabreeze-genomics)

[![Anaconda-Server Badge](https://anaconda.org/bioconda/seabreeze-genomics/badges/version.svg)](https://anaconda.org/bioconda/seabreeze-genomics)

_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](https://barricklab.github.io/seabreeze) 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](https://barricklab.org/twiki/bin/view/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](https://github.com/barricklab/seabreeze/blob/main/contributing.md).