castgen

R
CRAN
Conservation
Population Genetics
Sampling
R package for estimating sample sizes to capture genetic diversity in breeding populations

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

Overview

castgen provides methods for estimating the number of individuals to sample from a population in order to capture a predefined percentage of genetic diversity. Originally developed for the American chestnut landscape genomics project, it’s useful for conservation genetics and breeding program design.

Key Features

  • VCF or Matrix Input — Accepts VCF files or genotype matrices
  • Fast Computation — Parallel processing support
  • Confidence Intervals — Statistical bounds on sample size estimates
  • R Reimplementation — Much faster than the original Python version

Use Cases

  • Conservation genetics — Minimum sample size for seed banks or germplasm collections
  • Breeding programs — Plan crossing schemes that maintain diversity
  • Population studies — Optimize sampling strategies for surveys

Installation

install.packages("castgen")

Citation

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