text: 2.1.
  Genome sequencing, assembly and validation
  DNA shotgun libraries with average insert sizes of 1.6 and 6.5 kb were constructed in pUC118 (TaKaRa), whereas a fosmid library with average insert size of 37 kb was constructed in pCC1FOS (EPICENTRE) as described previously.18,19 A total of 50 400 clones (34 560, 10 752 and 5088 clones from libraries with 1.6, 6.5 and 37 kb inserts, respectively) were subjected to sequencing from both ends of the inserts on either ABI 3730xl DNA Analyzer (Applied Biosystems) or Base Station DNA Fragment Analyzer BST-0100 (MJ Research, Inc.). Sequence reads were trimmed at a threshold quality value of 20 by Phred and assembled by Phrap and CONSED assembly tools.20,21 For alignment and validation of contigs, Optical Mapping (OpGen) was used. Gaps between contigs were closed by sequencing PCR products, which bridge two neighboring contigs. Finally, each base of K. setae NBRC 14216T genome was ensured to be sequenced from multiple clones and from both directions with Phrap quality score >=70 or from one direction with Phrap quality score >=40. Chromosomal terminus was determined after attaching adenine and thymine homopolymers to the naked 3' ends of the chromosome as described previously.5
  
entities: ['chromosome']
entities: Cellular_component
entities: PMC-2993542-sec-03_T3