论文信息 - CIRCUS: a package for Circos display of structural genome variations from paired-end and mate-pair sequencing data

CIRCUS: a package for Circos display of structural genome variations from paired-end and mate-pair sequencing data

BackgroundDetection of large genomic rearrangements, such as large indels, duplications or translocations is now commonly achieved by next generation sequencing (NGS) approaches. Recently, several tools have been developed to analyze NGS data but the resulting files are difficult to interpret without an additional visualization step. Circos (Genome Res, 19:1639–1645, 2009), a Perl script, is a powerful visualization software that requires setting up numerous configuration files with a large number of parameters to handle. R packages like RCircos (BMC Bioinformatics, 14:244, 2013) or ggbio (Genome Biol, 13:R77, 2012) provide functions to display genomic data as circular Circos-like plots. However, these tools are very general and lack the functions needed to filter, format and adjust specific input genomic data.ResultsWe implemented an R package called CIRCUS to analyze genomic structural variations. It generates both data and configuration files necessary for Circos, to produce graphs. Only few R pre-requisites are necessary. Options are available to deal with heterogeneous data, various chromosome numbers and multi-scale analysis.ConclusionCIRCUS allows fast and versatile analysis of genomic structural variants with Circos plots for users with limited coding skills.

[1] E. Birney,et al. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. , 2008, Genome research.

[2] Hongen Zhang,et al. RCircos: an R package for Circos 2D track plots , 2013, BMC Bioinformatics.

[3] R Core Team,et al. R: A language and environment for statistical computing. , 2014 .

[4] Erik L. L. Sonnhammer,et al. ChromoWheel: a new spin on eukaryotic chromosome visualization , 2004, Bioinform..

[5] D. Cook,et al. ggbio: an R package for extending the grammar of graphics for genomic data , 2012, Genome Biology.

[6] Kai Ye,et al. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads , 2009, Bioinform..

[7] Steven J. M. Jones,et al. Circos: an information aesthetic for comparative genomics. , 2009, Genome research.

[8] Emmanuel Barillot,et al. SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data , 2010, Bioinform..