Abstract
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.
Highlights
Detection of large genomic rearrangements, such as large indels, duplications or translocations is commonly achieved by generation sequencing (NGS) approaches
In order to provide fast visual analyses of structural genome variations, we have developed a wrapper of Circos for the R langage which supports a subset of Circos functionnalities and shelters the user from managing the large number of parameters in Circos configuration files
Implementation Besides the positions and the significance of the structural rearrangements, additional data can be informative on the final image display: local coverage in reads, Copy Number Variation (CNV) inference or/and gene annotations
Summary
Detection of large genomic rearrangements, such as large indels, duplications or translocations is commonly achieved by generation sequencing (NGS) approaches. * Correspondence: delphine.naquin@cgm.cnrs-gif.fr 1Plateforme Intégrée IMAGIF – CNRS, Avenue de la Terrasse, Gif sur Yvette 91198, France Full list of author information is available at the end of the article tools [1,2,3] have been developed, displaying each variation as a link between positions on a circular ideogram. In order to provide fast visual analyses of structural genome variations, we have developed a wrapper of Circos for the R langage which supports a subset of Circos functionnalities and shelters the user from managing the large number of parameters in Circos configuration files.
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