Genomic and phenotypic characterization of Salmonella enterica subsp. enterica serovar Newport water isolates
Libraries were prepared using the Roche KAPA HyperPrep DNA library kit with Kapa Unique Dual-Indexed adapters following manufacturers recommendations. Completed libraries were QCd and quantified using a combination of Qubit dsDNA HS and Agilent 4200 TapeStation HS DNA1000 assays. The libraries were normalized to a consistent concentration and equal volumes of the normalized libraries pooled, and the pool was quantified using the Invitrogen Collibri Quantification qPCR kit. The combined pool was loaded onto one lane of a NovaSeq S4 flow cell using the Xp loading kit & workflow. Sequencing was performed in a 2x150bp paired end format using a NovaSeq 6000 v1.5 300 cycle reagent kit. Base calling was done by Illumina Real Time Analysis (RTA) v1.18.54 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.20.0.