WGS of Escherichia  coli:AS003587-HiSeq-2000
Quality control of isolated bacterial DNA was performed using a Qubit 2.0 Fluorometer (Qubit dsDNA BR Assay Kit, Life Technologies) and an Agilent 2200 TapeStation (Genomic DNA ScreenTape, Agilent Technolgies) before library preparation. NGS libraries were prepared in 96 well format using NexteraXT DNA Sample Preparation Kit and NexteraXT index kit for 96 indexes (Illumina) according to the manufacturers protocol. The generated sequencing libraries were quantified with the qPCR-based approach using the KAPA SYBR FAST qPCR MasterMix Kit (Peqlab) on a ViiA 7 Real-Time PCR System (Life Technologies). 50 samples were pooled by lane for paired-end sequencing (2x 101 bp) on Illumina HiSeq 2000 or HiSeg 2500 using TruSeq PE cluster v3 and TruSeq SBS v3 sequencing chemistry (Illumina).