Sierra SARS-CoV-2 sequence and antiviral resistance analysis program

•Sierra SARS-CoV-2 provides quality control and annotation for viral genomic data.•Sierra SARS-CoV-2 is highly concordant with established sequence analysis programs.•300 SARS-CoV-2 Spike mutations reduce susceptibility to monoclonal antibodies.•Approximately 20 RdRP and Mpro mutations reduce antiviral susceptibility in vitro.•Sierra SARS-CoV-2 has susceptibility data for 88% of Spike RBD mutation patterns.