Developer

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Jeffrey Barrick edited this page May 19, 2024 · 3 revisions

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

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++]