BPGA: an interactive Shiny application for basic population genetic analysis of genotype data

Joan Fibla 

Background: Population structure and ancestry inference are routine in human genetics, yet remain inconvenient for non-experts because canonical tools (PLINK, GCTA, ADMIXTURE) require command-line expertise and careful data management.
Results: BPGA (Basic Population Genetic Analysis) is an open-source R/Shiny application that provides an interactive workflow for educational and exploratory population genetic analyses on datasets in PLINK binary format. BPGA executes LD‑pruned PCA, genome‑wide Fst scans, and ADMIXTURE clustering from a guided interface, and it can optionally merge user data with curated worldwide reference panels (1000 Genomes Project and Human Genome Diversity Project). The app produces publication‑ready figures (PNG/HTML), interactive views (plotly/leaflet), and preserves logs for reproducibility.
Availability: Source code is available at https://github.com/jfibla/BPGA-a-Shiny-app-to-perform-Basic-Population-Genetic-Analysis under the Apache‑2.0 license. A hosted demo is also available at http://15.188.54.171:3838/bpga_app/.
Conclusions: BPGA lowers the barrier between raw genotype data and interpretable population‑genetic summaries for research and teaching, while keeping analyses transparent and reproducible.