seabreeze

seabreeze is a tool for the comprehensive analysis of structural variant (SV) mutations in bacterial resequencing experiments; it automates and unites several analyses into a single, easy-to-use pipeline. seabreeze uses a combination of existing packages and custom scripts, with Snakemake to manage dependencies and the workflow.

• To get started, please refer to the installation.
• For an overview of the commands, please see usage. Each command can generate several output files, however most users will usually only find a subset of them relevant. These have been highlighted in the usage itself. A more extensive documentation of the other output files is on the output page. Wherever the output corresponds to a file type/format from an existing package, the user is redirected to the respective package's documentation. Wherever the output corresponds a new file format specific to seabreeze, it is described on the output page.
• If you would like to learn how to use seabreeze, give the tutorial a try.
• seabreeze is available under the MIT License, and source code is on GitHub.
• If you have any questions, want to report bugs/error or submit a request for a new feature, please start a new GitHub issue.
• See other software to analyse bacterial genomes from the Barrick Lab at the University of Texas at Austin
• Contact the creators at irazibbu@utexas.edu or jbarrick@cm.utexas.edu.