title: CAR: contig assembly of prokaryotic draft genomes using rearrangements.
abstract: BACKGROUND
  Next generation sequencing technology has allowed efficient production of draft genomes for many organisms of interest. However, most draft genomes are just collections of independent contigs, whose relative positions and orientations along the genome being sequenced are unknown. Although several tools have been developed to order and orient the contigs of draft genomes, more accurate tools are still needed.
  
  
  RESULTS
  In this study, we present a novel reference-based contig assembly (or scaffolding) tool, named as CAR, that can efficiently and more accurately order and orient the contigs of a prokaryotic draft genome based on a reference genome of a related organism. Given a set of contigs in multi-FASTA format and a reference genome in FASTA format, CAR can output a list of scaffolds, each of which is a set of ordered and oriented contigs. For validation, we have tested CAR on a real dataset composed of several prokaryotic genomes and also compared its performance with several other reference-based contig assembly tools. Consequently, our experimental results have shown that CAR indeed performs better than all these other reference-based contig assembly tools in terms of sensitivity, precision and genome coverage.
  
  
  CONCLUSIONS
  CAR serves as an efficient tool that can more accurately order and orient the contigs of a prokaryotic draft genome based on a reference genome. The web server of CAR is freely available at http://genome.cs.nthu.edu.tw/CAR/ and its stand-alone program can also be downloaded from the same website.
authors.affiliation: Department of Computer Science, National Tsing Hua University, Hsinchu, 300, Taiwan. cllu@cs.nthu.edu.tw.
authors.forename: Chin Lung
authors.initials: CL
authors.lastname: Lu
authors.affiliation: Department of Computer Science, National Tsing Hua University, Hsinchu, 300, Taiwan. holystu@gmail.com.
authors.forename: Kun-Tze
authors.initials: KT
authors.lastname: Chen
authors.affiliation: Department of Computer Science, National Tsing Hua University, Hsinchu, 300, Taiwan. happyday5296@hotmail.com.
authors.forename: Shih-Yuan
authors.initials: SY
authors.lastname: Huang
authors.affiliation: Department of Chemistry, National Cheng Kung University, Tainan City, 701, Taiwan. hchiu@mail.ncku.edu.tw.
authors.forename: Hsien-Tai
authors.initials: HT
authors.lastname: Chiu
mesh_terms: D000465:Algorithms; D002874:Chromosome Mapping / Q000379:methods*; D019295:Computational Biology / Q000379:methods*; D020451:Contig Mapping / Q000379:methods*; D015321:Gene Rearrangement; D016678:Genome; D011387:Prokaryotic Cells; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software