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Welcome to the breseq wiki!

This Wiki provides instructions to get set up for contributing to breseq development and a roadmap for ongoing coding projects. If you are looking for help using breseq to analyze your data, please see the online documentation instead of these pages.

Developer Quickstart

Developer Information

• Code of Conduct
• Build Status (via Travis CI)
• List of Proposed Coding Projects

In-Progress Coding Projects

• Add Interactivity to HTML output [Core:HTML/Javascript/C++]
• Predict copy number variation [Test:R→Core:C++]
• Compare across samples to improve predictions of low-frequency variants [Test:Python/R→Core:C++]

Available Coding Projects

• Parallelize breseq execution [Core:C++]
• Update/improve Circos visualization [Extension:Python/Javascript]
• Treatment similarity/specificity statistics [Extension:Python/R]
• Summarize data quality/coverage across many runs [Extension:Python/R]
• Phylogenetic tree generation [Extension:R]
• Detect discontinuity (soft-clipping) evidence [Core:C++]
• Predict structural variation from mate-pair mapping [Test:Python→Core:C++]