Instrument: Illumina HiSeq 2000
Strategy: WGS
Source: GENOMIC
Selection: size fractionation
Layout: PAIRED
Construction protocol: Genomic DNAs (gDNA) from the targeted bacteria were extracted from overnight cultures using KAPA enzyme lysis buffer and Qiagen DNeasy Blood and Tissue kit. Subsequently, gDNA was fragmented to an average size of 200-450 bp using Diogenode Bioruptor NGS or Covaris E220. Fragmented gDNA was then converted into sequencing libraries using KAPA HTP library preparation kit (Illumina platform), which was performed on the automated liquid handling platform Bravo Option B (Agilent). Briefly, fragmented double strand gDNA molecules were end-repaired, adenylated, and ligated to NEXTflex-96 DNA Barcode indexed sequencing adaptors (Bioo Scientific). This set of DNA barcode allowed us to multiplex up to 96 sequencing samples in a single sequencing run. Following the ligation, indexed dsDNA fragments were size selected (AmPure beads based) and PCR amplified. Finally, indexed sequencing libraries were pooled and sequenced on Illumina Hiseq2000 with PE100 plus index read. Once sequenced, raw sequencing reads were deplexed using in-house NGS data processing pipeline.