SNeP

CNVkit -- Python toolkit for detecting copy number variants (CNVs) from targeted DNA sequencing data (hybrid capture, amplicon) and whole-genome sequencing (WGS). Leverages both on-target and off-targ

1 shared topic • 2 shared operations

Harvest Tools — core genome phylogenomics suite for rapid whole-genome alignment, SNP extraction, and phylogenetic tree inference from closely related microbial genomes. Parsnp performs MUMmer-based c

1 shared topic • 2 shared operations

LINX — structural variant annotation and visualization tool from the Hartwig Medical Foundation hmftools suite. Interprets structural variants and copy number data to classify driver events including

1 shared topic • 2 shared operations

Use when working with odgi — the optimized dynamic genome/graph implementation toolkit — for pangenome variation graph manipulation, sorting, visualization, and analysis. Converts GFA graphs to effici

1 shared topic • 2 shared operations

rMVP GWAS analysis for plant genomics. Use when running genome-wide association studies, GWAS models (GLM, MLM, FarmCPU), SNP genotype formatting, kinship matrix calculation, population structure PCA,

1 shared topic • 2 shared operations