title: A cost-effective and universal strategy for complete prokaryotic genomic sequencing proposed by computer simulation.
abstract: BACKGROUND
  Pyrosequencing techniques allow scientists to perform prokaryotic genome sequencing to achieve the draft genomic sequences within a few days. However, the assemblies with shotgun sequencing are usually composed of hundreds of contigs. A further multiplex PCR procedure is needed to fill all the gaps and link contigs into complete chromosomal sequence, which is the basis for prokaryotic comparative genomic studies. In this article, we study various pyrosequencing strategies by simulated assembling from 100 prokaryotic genomes.
  
  
  RESULTS
  Simulation study shows that a single end 454 Jr. run combined with a paired end 454 Jr. run (8 kb library) can produce: 1) ~90% of 100 assemblies with < 10 scaffolds and ~95% of 100 assemblies with < 150 contigs; 2) average contig N50 size is over 331 kb; 3) average single base accuracy is > 99.99%; 4) average false gene duplication rate is < 0.7%; 5) average false gene loss rate is < 0.4%.
  
  
  CONCLUSIONS
  A single end 454 Jr. run combined with a paired end 454 Jr. run (8 kb library) is a cost-effective way for prokaryotic whole genome sequencing. This strategy provides solution to produce high quality draft assemblies for most of prokaryotic organisms within days. Due to the small number of assembled scaffolds, the following multiplex PCR procedure (for gap filling) would be easy. As a result, large scale prokaryotic whole genome sequencing projects may be finished within weeks.
authors.affiliation: School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong, China. fcleung@hkucc.hku.hk.
authors.forename: Jingwei
authors.initials: J
authors.lastname: Jiang
authors.forename: Jun
authors.initials: J
authors.lastname: Li
authors.forename: Hoi Shan
authors.initials: HS
authors.lastname: Kwan
authors.forename: Chun Hang
authors.initials: CH
authors.lastname: Au
authors.forename: Patrick Tik
authors.initials: PT
authors.lastname: Wan Law
authors.forename: Lei
authors.initials: L
authors.lastname: Li
authors.forename: Kai Man
authors.initials: KM
authors.lastname: Kam
authors.forename: Julia Mei
authors.initials: JM
authors.lastname: Lun Ling
authors.forename: Frederick C
authors.initials: FC
authors.lastname: Leung