ContigScape: a Cytoscape plugin facilitating microbial genome gap closing

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• 作者：Biao Tang (1) (2)
  Qi Wang (3) (6)
  Minjun Yang (2)
  Feng Xie (3)
  Yongqiang Zhu (2)
  Ying Zhuo (3)
  Shengyue Wang (2)
  Hong Gao (3)
  Xiaoming Ding (1)
  Lixin Zhang (3)
  Guoping Zhao (1) (2) (4) (5)
  Huajun Zheng (2)
  
• 关键词：ContigScape ; Repeat contig ; Microbial ; Visualization ; Linkage ; Gap closing
• 刊名：BMC Genomics
• 出版年：2013
• 出版时间：December 2013
• 年：2013
• 卷：14
• 期：1
• 全文大小：1557KB
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• 作者单位：Biao Tang (1) (2)
  Qi Wang (3) (6)
  Minjun Yang (2)
  Feng Xie (3)
  Yongqiang Zhu (2)
  Ying Zhuo (3)
  Shengyue Wang (2)
  Hong Gao (3)
  Xiaoming Ding (1)
  Lixin Zhang (3)
  Guoping Zhao (1) (2) (4) (5)
  Huajun Zheng (2)
  
  1. State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai, 200433, China
  2. Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, 201203, China
  3. CAS Key Laboratory of Pathogenic Microbiology & Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100190, China
  6. Graduate School of Chinese Academy of Sciences, Beijing, 100049, China
  4. CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
  5. Department of Microbiology and Li KaShing Institute of Health SciencesThe Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
  

文摘

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.