Rapid genotyping of targeted viral samples using Illumina short-read sequencing data
Libraries were prepared with NEXTFLEX Variant-Seq SARS-CoV-2 Kit (For Illumina Platforms) (Perkin Elmer, Waltham, MA, USA). The libraries were processed in an Illumina MiSeq platform using a MiSeq Reagent Kit v3 (Illumina, San Diego, CA, USA) following the manufacturers instructions.