seabreeze: A Pipeline for Analyzing Structural Variation Between Bacterial Genome Assemblies
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2025
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| author | Zibbu, Ira Wilke, Claus O. Barrick, Jeffrey E. |
| author_facet | Zibbu, Ira Wilke, Claus O. Barrick, Jeffrey E. |
| contents | <p dir="auto"><em>seabreeze</em> 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:</p> <ul> <li>Compute size difference between genomes</li> <li>Predict the location of insertion sequences</li> <li>Predict structural mutations (inversions, deletions, translocations, duplications)</li> <li>Generate intuitive synteny plots to visualise structural variation</li> <li>Analyse the effect of structural mutations on the balance of the two replichores</li> <li>Predict the putative mechanism of inversions and deletions</li> <li>Annotate the genes contained in the mutated regions</li> </ul> <p dir="auto">Please refer to the <a href="https://barricklab.github.io/seabreeze" rel="nofollow">official documentation</a> for information on installation and usage.</p> <p dir="auto"><em>seabreeze</em> was developed at the <a href="https://barricklab.org/twiki/bin/view/Lab" rel="nofollow">Barrick Lab</a> at the University of Texas at Austin.</p> |
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| id | zenodo_https___doi_org_10_5281_zenodo_15994089 |
| institution | Zenodo |
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| publishDate | 2025 |
| publisher | Zenodo |
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| spellingShingle | seabreeze: A Pipeline for Analyzing Structural Variation Between Bacterial Genome Assemblies Zibbu, Ira Wilke, Claus O. Barrick, Jeffrey E. <p dir="auto"><em>seabreeze</em> 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:</p> <ul> <li>Compute size difference between genomes</li> <li>Predict the location of insertion sequences</li> <li>Predict structural mutations (inversions, deletions, translocations, duplications)</li> <li>Generate intuitive synteny plots to visualise structural variation</li> <li>Analyse the effect of structural mutations on the balance of the two replichores</li> <li>Predict the putative mechanism of inversions and deletions</li> <li>Annotate the genes contained in the mutated regions</li> </ul> <p dir="auto">Please refer to the <a href="https://barricklab.github.io/seabreeze" rel="nofollow">official documentation</a> for information on installation and usage.</p> <p dir="auto"><em>seabreeze</em> was developed at the <a href="https://barricklab.org/twiki/bin/view/Lab" rel="nofollow">Barrick Lab</a> at the University of Texas at Austin.</p> |
| title | seabreeze: A Pipeline for Analyzing Structural Variation Between Bacterial Genome Assemblies |
| url | https://doi.org/10.5281/zenodo.15994089 |