RVFscan provides a multi-annotation system, including a curated VFGs database composed of 27470 representative VFG sequences, VF functional and clinical characteristics, and a pipeline for identifying the important VFGs based on clinical metagenomic next-generation sequencing (mNGS) short-reads data. This tool can be used to identify 2456 VFGs of 24 pathogenic bacteria at one time.

In RVFscan principle, the mNGS short reads were mapped in single-end mode to the indexed clinical VFGs reference database, and then the results are evaluated with the gene criteria value which based on the similarity matrix from comparison of orthologs and paralogs.