Title : ContigScape: a Cytoscape plugin facilitating microbial genome gap closing - Tang_2013_BMC.Genomics_14_289
Author(s) : Tang B , Wang Q , Yang M , Xie F , Zhu Y , Zhuo Y , Wang S , Gao H , Ding X , Zhang L , Zhao G , Zheng H
Ref : BMC Genomics , 14 :289 , 2013
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.

PubMedSearch : Tang_2013_BMC.Genomics_14_289
PubMedID: 23627759
Gene_locus related to this paper: myctu-cut3 , myctu-cutas1 , myctu-cutas2 , myctu-Rv0160c , myctu-Rv1069c , myctu-RV1215C , myctu-Rv2045c , myctu-RV3452 , myctu-Rv3802c , amyor-r4tdn6 , amyor-r4sys4 , amyor-r4svp2 , amyor-r4t193 , amyor-r4t8c7 , amyor-r4t8w6 , amyor-r4t1x8 , amyor-r4stv4 , amyor-r4t7z6 , 9pseu-r4sx12

Related information

Gene_locus myctu-cut3    myctu-cutas1    myctu-cutas2    myctu-Rv0160c    myctu-Rv1069c    myctu-RV1215C    myctu-Rv2045c    myctu-RV3452    myctu-Rv3802c    amyor-r4tdn6    amyor-r4sys4    amyor-r4svp2    amyor-r4t193    amyor-r4t8c7    amyor-r4t8w6    amyor-r4t1x8    amyor-r4stv4    amyor-r4t7z6    9pseu-r4sx12
Gene_locus_frgt myctu-cut3    myctu-cutas1    myctu-cutas2    myctu-Rv0160c    myctu-Rv1069c    myctu-RV1215C    myctu-Rv2045c    myctu-RV3452    myctu-Rv3802c    amyor-r4tdn6    amyor-r4sys4    amyor-r4svp2    amyor-r4t193    amyor-r4t8c7    amyor-r4t8w6    amyor-r4t1x8    amyor-r4stv4    amyor-r4t7z6    9pseu-r4sx12    myctu-Rv1104

Citations formats

Tang B, Wang Q, Yang M, Xie F, Zhu Y, Zhuo Y, Wang S, Gao H, Ding X, Zhang L, Zhao G, Zheng H (2013)
ContigScape: a Cytoscape plugin facilitating microbial genome gap closing
BMC Genomics 14 :289

Tang B, Wang Q, Yang M, Xie F, Zhu Y, Zhuo Y, Wang S, Gao H, Ding X, Zhang L, Zhao G, Zheng H (2013)
BMC Genomics 14 :289