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Developer
Jeffrey Barrick edited this page May 19, 2024
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This part of the Wiki provides instructions to get set up for contributing to breseq development and a roadmap for ongoing coding projects.
Developer Information
- Developer Quickstart
- Developer Installation
- Code of Conduct
- List of Proposed Coding Projects
- Coding Style Guide
In-Progress Coding Projects
- Add Interactivity to HTML output [Core:HTML/Javascript/C++]
- Parallelize breseq execution [Core:C++]
- Predict copy number variation [Test:R→Core:C++]
- Detect discontinuity (soft-clipping) evidence [Core:C++]
Available Coding Projects
- Compare across samples to improve predictions of low-frequency variants [Test:Python/R→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]
- Predict structural variation from mate-pair mapping [Test:Python→Core:C++]
Quick Start
Installation
Test Drive
More Options
Usage: breseq
Usage: gdtools
More Information
GenomeDiff File Format
Reference Sequence File Formats
Output
Methods
Bibliography
FAQ
More Examples
Tutorial: Clones
Tutorial: Populations
Tutorial: Barcoded/Targeted
Tutorial: Curation
Contribute
Developer