cmd

var RootCmd = &cobra.Command{
	Use:   "groot",
	Short: "annotate Antibiotic Resistance Genes (ARGs) from metagenomes using variation graphs",
	Long: `
#####################################################################################
		GROOT: Graphing Resistance genes Out Of meTagenomes
#####################################################################################

 GROOT is a tool to type Antibiotic Resistance Genes (ARGs) in metagenomic samples.

 It combines variation graph representation of gene sets with an LSH indexing scheme
 to allow for fast classification of metagenomic reads. Subsequent hierarchical local
 alignment of classified reads against graph traversals facilitates accurate reconstruction
 of full-length gene sequences using a simple scoring scheme.

 GROOT can output an ARG alignment file, as well as a typing report and the variation graphs
 with aligned reads.`,
}