title: ContigScape: a Cytoscape plugin facilitating microbial genome gap closing.
abstract: BACKGROUND
  With the emergence of next-generation sequencing, the availability of prokaryotic genome sequences is expanding rapidly. A total of 5,276 genomes have been released since 2008, yet only 1,692 genomes were complete. The final phase of microbial genome sequencing, particularly gap closing, is frequently the rate-limiting step either because of complex genomic structures that cause sequence bias even with high genomic coverage, or the presence of repeat sequences that may cause gaps in assembly.
  
  
  RESULTS
  We have developed a Cytoscape plugin to facilitate gap closing for high-throughput sequencing data from microbial genomes. This plugin is capable of interactively displaying the relationships among genomic contigs derived from various sequencing formats. The sequence contigs of plasmids and special repeats (IS elements, ribosomal RNAs, terminal repeats, etc.) can be displayed as well.
  
  
  CONCLUSIONS
  Displaying relationships between contigs using graphs in Cytoscape rather than tables provides a more straightforward visual representation. This will facilitate a faster and more precise determination of the linkages among contigs and greatly improve the efficiency of gap closing.
authors.affiliation: State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai 200433, China.
authors.forename: Biao
authors.initials: B
authors.lastname: Tang
authors.forename: Qi
authors.initials: Q
authors.lastname: Wang
authors.forename: Minjun
authors.initials: M
authors.lastname: Yang
authors.forename: Feng
authors.initials: F
authors.lastname: Xie
authors.forename: Yongqiang
authors.initials: Y
authors.lastname: Zhu
authors.forename: Ying
authors.initials: Y
authors.lastname: Zhuo
authors.forename: Shengyue
authors.initials: S
authors.lastname: Wang
authors.forename: Hong
authors.initials: H
authors.lastname: Gao
authors.forename: Xiaoming
authors.initials: X
authors.lastname: Ding
authors.forename: Lixin
authors.initials: L
authors.lastname: Zhang
authors.forename: Guoping
authors.initials: G
authors.lastname: Zhao
authors.forename: Huajun
authors.initials: H
authors.lastname: Zheng
mesh_terms: D020451:Contig Mapping / Q000379:methods*; D030561:Databases, Nucleic Acid; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods*; D006801:Humans; D008969:Molecular Sequence Data; D012091:Repetitive Sequences, Nucleic Acid; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software