WGS of Salmonella Enteritidis: raw inshell pistachios
For each sample, 10 ng genomic DNA was converted to barcode-indexed sequencing libraries using the Seqwell plexWell LP384 Library Preparation Kit for Illumina Sequencing Platforms (seqWell, Beverly, MA). The libraries were amplified with 8 PCR cycles and analyzed with a Bioanalyzer 2100 instrument (Agilent, Santa Clara, CA), quantified by fluorometry on a Qubit instrument (LifeTechnologies, Carlsbad, CA), and combined in two pools at equimolar ratios. The library pool was quantified by qPCR with a Kapa Library-Quant kit (Kapa Biosystems/Roche, Basel Switzerland) and sequenced on an Illumina NovaSeq system (Illumina) run with paired-end 150 bp reads.