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首页> 外文期刊>BMC Genomics >ContigScape: a Cytoscape plugin facilitating microbial genome gap closing
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ContigScape: a Cytoscape plugin facilitating microbial genome gap closing

机译：ContigScape：一个Cytoscape插件，可促进微生物基因组缺口的闭合

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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.
机译：背景技术随着下一代测序的出现，原核基因组序列的可用性正在迅速扩展。自2008年以来，共发布了5,276个基因组，但仅完成了1,692个基因组。微生物基因组测序的最后阶段，尤其是缺口关闭，通常是限速步骤，这是因为复杂的基因组结构甚至在高基因组覆盖率下也导致序列偏倚，或者存在重复序列可能会导致装配缺口。结果我们开发了一个Cytoscape插件，以促进缺口关闭，以获取微生物基因组的高通量测序数据。该插件能够交互显示来自各种测序格式的基因组重叠群之间的关系。质粒和特殊重复序列（IS元件，核糖体RNA，末端重复序列等）的重叠序列也可以显示。结论使用Cytoscape中的图形而不是表显示重叠群之间的关系可以提供更直接的视觉表示。这将有助于更快，更精确地确定重叠群之间的联系，并大大提高缺口闭合的效率。

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