The Virus Reference-based Assembly Pipeline and IDentification (vRAPID) tool runs the assembly, consensus calling, and annotation of viral pathogen genomes. vRAPID relies on data structures and naming conventions used by the Center for Research on Influenza Pathogenesis and Transmission (CRIPT) and the Mount Sinai Pathogen Surveillance Program (MS-PSP) at the Icahn School of Medicine at Mount Sinai. vRAPID is an expansion of the COVID_pipe pipeline that was written by Mitchell Sullivan in the Bakel Lab. Complete documentation is available here.

{"references": ["https://zenodo.org/record/3775031", "https://doi.org/10.1126/science.abc1917"]}