title: CIRCUS: a package for Circos display of structural genome variations from paired-end and mate-pair sequencing data.
abstract: BACKGROUND
  Detection 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.
  
  
  RESULTS
  We 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.
  
  
  CONCLUSIONS
  CIRCUS allows fast and versatile analysis of genomic structural variants with Circos plots for users with limited coding skills.
authors.affiliation: Plateforme Intégrée IMAGIF - CNRS, Avenue de la Terrasse, Gif sur Yvette 91198, France. delphine.naquin@cgm.cnrs-gif.fr.
authors.forename: Delphine
authors.initials: D
authors.lastname: Naquin
authors.forename: Yves
authors.initials: Y
authors.lastname: d'Aubenton-Carafa
authors.forename: Claude
authors.initials: C
authors.lastname: Thermes
authors.forename: Maud
authors.initials: M
authors.lastname: Silvain
mesh_terms: D016678:Genome; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D012985:Software Design