NEBnext library construction and sequencing for SARS-CoV-2:Adapting COVID-19 ARTIC protocol v1

This protocol describes the procedure for generating cDNA from SARS-CoV-2 viral nucleic acid extracts and subsequently producing amplicons tiling the viral genome sequencing. It uses the V3 nCov-2019 primers from the ARTIC network. This is followed by library construction using Nextera Flex, which we found to save 9h of hands on time as compared with original protocol that uses TruSeq for library contstruction. It also describes the pooling of samples and quantitation, prior to sequencing on the Illumina Miseq. It is adapted from the nCov-2019 sequencing protocol from Quick and colleagues, which can be found here: