Bioinformatics Tools for Breeding Applications
Open-source software for plant and animal genomics
Bioinformatics Tools for Breeding Applications
Open-source software designed to make genomic analysis more accessible for plant and animal breeding programs.
About This Site
This site provides bioinformatics tools, tutorials, and workshop materials for genomic applications in breeding. The tools span variant calling, population genetics, genomic selection, and data visualization — built in R, Python, and Rust.
Tools
Open-source software packages for genomic data analysis. Each tool includes documentation, installation guides, and example workflows.
Tutorials
Step-by-step guides for common bioinformatics tasks. Learn at your own pace with code examples and sample data.
Workshops
Materials from hands-on workshops including setup instructions, slides, and exercises.
Featured Tools
BIGapp · R Shiny
User-friendly web app for genomic analysis—GWAS, genomic selection, PCA, and more—without command-line tools. Supports diploid and polyploid species.
BIGapp::run_app()BIGr · R Package (CRAN)
Core genomic analysis functions for diploid and polyploid breeding programs. The computational backbone for BIGapp.
install.packages("BIGr")Documentation · GitHub · CRAN
castgen · R Package (CRAN)
Estimate sample sizes needed to capture genetic diversity in breeding or conservation populations.
install.packages("castgen")Documentation · GitHub · CRAN
Binx · Rust CLI
Fast command-line tool for polyploid and diploid genomic analysis, built in Rust for performance.
Tool Publications
Sandercock A.M., Peel M.D., Taniguti C.H., et al. (2025). BIGapp: A User-Friendly Genomic Tool Kit Identified Quantitative Trait Loci for Creeping Rootedness in Alfalfa. The Plant Genome. DOI: 10.1002/tpg2.70067
Sandercock A.M., Westbrook J.W., Zhang Q., Holliday J.A. (2024). A genome-guided strategy for climate resilience in American chestnut restoration populations. PNAS 121(30) e2403505121. DOI: 10.1073/pnas.2403505121
Contact & Collaboration
Questions about the tools or interested in collaborating? Get in touch or open an issue on the relevant GitHub repository.