Whole genome sequencing of clinical and environmental strains of Burkholderia pseudomallei
The paired-end sequencing libraries were prepared from the QC passed genomic DNA samples using Illumina TruSeq Nano DNA Library Prep Kit. Briefly, approximately 200 ng of DNA was fragmented by Covaris M220 to generate a mean fragment distribution of 350bp. Covaris shearing generates dsDNA fragments with 3' or 5' overhangs. The fragments were then subjected to end-repair. This process converts the overhangs resulting from fragmentation into blunt ends using End Repair Mix. The 3' to 5' exonuclease activity of this mix removes the 3' overhangs and the 5' to 3' polymerase activity fills in the 5' overhangs followed by adapter ligation to the fragments. This strategy ensures a low rate of chimera (concatenated template) formation. The ligated products were size selected using AMPure XP beads. The size-selected products were PCR amplified with the index primer as described in the kit protocol indexing adapters were ligated to the ends of the DNA fragments, preparing them for hybridization onto a flow cell.