: Download and process the necessary reference data (e.g., NCBI nr or GTDB) using the download and prepare commands to ensure a robust foundation for classification.
: Use the RAT (Read Annotation Tool) to combine signals from your assembled MAGs and contigs, which provides a more "accurate and comprehensive view" of the microbiome. CAT Pack v 1.0
: Run the CAT (Contig Annotation Tool) or BAT (Bin Annotation Tool) to assign taxonomic identities to your sequences. : Download and process the necessary reference data (e