title: Draft genome of Pantoea agglomerans CPHN2
design: The  paired-end  sequencing  library  was  prepared  from  the  QC  passed  genomic  DNA  sample  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.  The PCR enriched library was analyzed on 4200 Tape Station system (Agilent Technologies) using high sensitivity D1000 Screen tape as per manufacturer instructions. After obtaining the Qubit concentration for the library and the mean peak size from Agilent Tape Station  profile,  the  PE  illumina  library  was  loaded  onto  NextSeq500  for  cluster  generation  and sequencing.  Paired-End  sequencing  allows  the  template  fragments  to  be  sequenced  in  both  the forward and reverse directions on NextSeq500. The kit reagents were used in binding of samples to complementary adapter oligoes on paired-end flow cell. 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.