title: Draft genome sequence of Klebsiella sp. strain SG01
design: The genomic DNA was extracted and purified from exponential stage of LB grown SGO1 using PureLinkTM genomic DNA isolation kit (Thermo Fisher Scientific, USA) followed by manufacturer protocol. The quality of the isolated genomic DNA was checked on 0.8% agarose gel using gel electrophoresis. Isolated DNA was quantified using Nano Drop (SPECTROstar Nano BMG Labtech). The paired end sequencing library was prepared from the purified genomic DNA sample using Illumina TruSeq Nano DNA Library Prep Kit (Illumina, USA). Briefly, approximately 200 ng of DNA was fragmented using Covaris M220 and generated a mean fragment length 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 per the manufacturer protocol. The PCR enriched libraries were analyzed on a 4200 Tape Station system (Agilent Technologies) using high sensitivity D1000 screen tapes as per manufacturer instructions. After obtaining the Qubit concentration for the library and the mean peak size from the Agilent Tape Station profile, the PE Illumina library was loaded onto NextSeq 500 for cluster generation and sequencing. Paired end sequencing allows the template fragments to be sequenced in both the forward and reverse directions on NextSeq 500 system. The Illumina TrueSeq kit reagents were used in the binding of samples to complementary adapter oligos on paired end flow cells. The adapters were designed to allow selective cleavage of the forward strands after re-synthesis of the reverse strand during sequencing. The copied reverse strand was then used to sequence from the opposite end of the fragment. The sequenced raw paired end data was processed using Trimmomatic v0.38 (http://www.usadellab.org/cms/?page_trimmomatic) to remove adapter sequences, low-quality sequences [reads with more than 10% quality threshold (QV) < 20 Phred score] and ambiguous reads (reads with unknown nucleotides N larger than 5%). Finally, the filtered high-quality reads of the SGO1 sample were de novo assembled into scaffolds using SPAdes version 3.11.1 (Nurk et al. 2013). The scaffolds, which were found to be shorter than 200 bases, were not considered for downstream analysis