title: WGS of SARS-CoV-2 isolated from patient swab.
design: Sequencing libraries were prepared from extracted patient RNAs using Qiagen QIAseq SARS-CoV-2 Primer Panel (Cat# 333896) according to the manufacturers instructions. Library fragment size was then checked using an Agilent Fragment Analyzer and quantified with qPCR using Collibri Library Quantification Kit (ThermoFisher, Cat#A38524500) on a BioRad CFX96 Touch Real-Time PCR Detection System. Quality-checked libraries were loaded onto an Illumina NextSeq 500 running with PE 150 cycles. Real-time base call (.bcl) files were converted to FASTQ files using Illumina bcl2fastq2 conversion software v2.17 (on CentOS 6.0 data storage and computation Linux servers). The genome mapping and variant calling were performed by CLC Genomics Workbench V21.0.1 with QIAseq SARS-CoV2 workflow V1.0. The resulting consensus sequences were then uploaded to Pangolin for lineage assignment.