Tools & Software

Open-source bioinformatics tools for plant and animal breeding

All tools are open-source and available on GitHub. Click on a tool for documentation, installation instructions, and examples.

A fast Rust-based CLI tool for polyploid and diploid genomic analysis

A user-friendly R Shiny app to analyze genomic data without command-line tools, supporting diploid and polyploid species

Core R package with genomic analysis functions for diploid and polyploid breeding programs

R package for estimating sample sizes to capture genetic diversity in breeding populations

Snakemake automated workflow for GATK variant calling pipeline

Quick Reference

Tool	Language	Status	Purpose	Install
Binx	Rust	Experimental	Fast polyploid CLI	GitHub Releases
BIGapp	R/Shiny	Stable	Genomic analysis web app	`BiocManager::install("Breeding-Insight/BIGapp")`
BIGr	R	Stable	Core genomic functions	`install.packages("BIGr")`
castgen	R	Stable	Sample size estimation	`install.packages("castgen")`
SimpleSnek	Python	Active	GATK variant calling	Clone from GitHub

Please open an issue on the relevant GitHub repository. When reporting bugs, include: