Crop Genomic Breeding machine (CropGBM) is a multifunctional program that integrates data preprocessing, population structure analysis, SNP selection, phenotype prediction, and data visualization. Has the following advantages:

  • Use LightGBM algorithm to quickly and accurately predict phenotype values and support GPU-accelerated training.
  • Supports selection and visualization of SNPs that are strongly related to phenotype.
  • Support PCA and t-SNE two dimensionality reduction algorithms to extract SNP information.
  • Support Kmeans and OPTICS two clustering algorithms to analyze the sample population structure.
  • Plot histograms of heterozygosity rate, deletion rate, and frequency of alleles for genotype data.

CropGBM was developed by Yuetong Xu in 2020.

Please read the tutorial for details!

Yuetong Xu
Yuetong Xu
PhD. Student