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seabreeze

seabreeze: A Pipeline for Analyzing Structural Variation Between Bacterial Genome Assemblies - Published in JOSS (2025)

https://github.com/barricklab/seabreeze

Science Score: 87.0%

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    DOI references
    Found 3 DOI reference(s) in README and JOSS metadata
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    JOSS paper metadata
    Published in Journal of Open Source Software

Keywords

bioinformatics-pipeline experimental-evolution long-read-sequencing structural-variation
Last synced: 6 months ago · JSON representation

Repository

seabreeze: A Pipeline for Analyzing Structural Variation Between Bacterial Genome Assemblies

Basic Info
Statistics
  • Stars: 1
  • Watchers: 1
  • Forks: 2
  • Open Issues: 7
  • Releases: 6
Topics
bioinformatics-pipeline experimental-evolution long-read-sequencing structural-variation
Created over 1 year ago · Last pushed 6 months ago

https://github.com/barricklab/seabreeze/blob/main/ 

# 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)

_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).

Owner

  • Name: Barrick Lab
  • Login: barricklab
  • Kind: organization
  • Location: Austin, TX

Barrick Lab at the University of Texas at Austin

JOSS Publication

seabreeze: A Pipeline for Analyzing Structural Variation Between Bacterial Genome Assemblies
Published
July 24, 2025
DOI
Volume 10, Issue 111, Page 8065
Authors
Ira Zibbu ORCID
Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America, School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala, India
Claus O. Wilke ORCID
Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, United States of America
Jeffrey E. Barrick ORCID
Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
Editor
Abhishek Tiwari ORCID
Tags
structural variation experimental evolution bacterial genomics Snakemake
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GitHub Events

Total
  • Create event: 11
  • Issues event: 10
  • Release event: 4
  • Delete event: 3
  • Issue comment event: 29
  • Push event: 97
  • Pull request event: 2
  • Fork event: 2
Last Year
  • Create event: 11
  • Issues event: 10
  • Release event: 4
  • Delete event: 3
  • Issue comment event: 29
  • Push event: 97
  • Pull request event: 2
  • Fork event: 2

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 9
  • Total pull requests: 2
  • Average time to close issues: 2 months
  • Average time to close pull requests: less than a minute
  • Total issue authors: 2
  • Total pull request authors: 1
  • Average comments per issue: 4.56
  • Average comments per pull request: 0.5
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 9
  • Pull requests: 2
  • Average time to close issues: 2 months
  • Average time to close pull requests: less than a minute
  • Issue authors: 2
  • Pull request authors: 1
  • Average comments per issue: 4.56
  • Average comments per pull request: 0.5
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • dr-joe-wirth (5)
  • JeanMainguy (4)
Pull Request Authors
  • ira-zibbu (2)
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