Whole genome sequencing of Escherichia coli : Food
Shotgun genomic libraries were prepared using the Illumina DNA Prep kit (Illumina cat. no. 20060060). Libraries were quantified by qPCR and sequenced on a MiSeq i100 25M flowcell with 301-cycle paired-end sequencing. FASTQ files were generated and demultiplexed using bcl2fastq v2.20 (Illumina). PhiX DNA was included as a spike-in control for nucleotide diversity, and quality scores were encoded in Sanger format (ASCII offset 33)