Raw reads: W34Y23Lul
DNAse treatment was performed to prevent bacterial unspecific amplification before library preparation for Miseq sequencing. The Illumina COVIDSeq Assay kit was used to generate the libraries. Samples from weeks 22, 23, 33, and 34 were amplified using the IDT Artic V4.1 NCOV-2019 Panel primers, while the remaining weeks were amplified using the IDT Artic V5.3.2 NCOV-2019 Panel primers. The resulting libraries were sequenced on the Illumina Miseq platform using the MiSeq Reagent Kit v3 (150-cycle) at the Functional Microbial Ecology Lab (FUME) within the Swedish University of Agriculture.