GenoBrew is a user-friendly R Shiny application for measuring marker panel efficiency according to dataset, help users optmize markers selection, perform basic relationship analysis, and visualization and curation of copy number variation (CNV) profiles. It includes built-in datasets for alfalfa genomic data exploration and analysis, designed to support breeders and researchers without requiring command-line expertise.
- Web-Based Interface: Run analyses directly in the browser — no command-line required.
- Select Markers module: Compare marker statistics derived from whole-genome sequencing (WGS), GBS, or other sequencing technology with a set marker panel.
- CNV Profiles module: Explore interactive visualizations and curation of copy number variation profiles across samples. Also visualize relationship statistics for families.
- Built-in datasets: Includes the Alfalfa F1 population dataset, ready to load for analysis. This dataset is publicly available and validated using the Alfalfa 3k DArTag marker panel.
- Upload your own data: Accepts VCF and CNV files in CSV/TSV/GZ formats alongside a custom marker panel CSV.
Loads a VCF file (or built-in WGS dataset) and a marker panel, then computes and displays:
- WGS marker count, panel marker count, common markers, and markers passing filters
- Interactive marker distribution plot
- Filters: minimum MAF, maximum missing data, depth range, heterozygosity range, maximum % CNV ≠ 2
- Genomic relationship plots
Loads Qploidy2 output files (or built-in dataset) and visualizes:
See more about Qplody2 in its repository.
- Genome-wide CNV profiles for combined samples
- BAF, zscore and CNV calls plots for single sample
- Curation of results by re-running HMM for specific samples with user-defined parameters
You can explore GenoBrew features accessing its shinyapps.io version, but the server has limited resources, for larger datasets you will need to install the app in our local computer.
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Install R (≥ 4.1.0) from CRAN.
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Install GenoBrew:
if (!require("remotes", quietly = TRUE)) install.packages("remotes")
remotes::install_github("Breeding-Insight/GenoBrew", dependencies = TRUE)- Launch the app:
GenoBrew::run_app()- The GenoBrew interface will open in your default web browser.
Access GenoBrew tutorial here.
If you use GenoBrew in research or breeding analyses, please cite it as:
Taniguti, C. H.; Chinchilla-Vargas, J.; Casa, Alexandra. GenoBrew: A user-friendly Shiny app for evaluating marker panel efficiency and visualizing CNV profiles. RRID: SCR_028314
GenoBrew development is supported by Breeding Insight, a USDA-funded initiative hosted at the University of Florida – IFAS.
This project is licensed under the Apache-2.0 license. See LICENSE for details.