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Open Access Highly Accessed Software

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

Delphine Naquin1*, Yves d’Aubenton-Carafa2, Claude Thermes2 and Maud Silvain2

Author Affiliations

1 Plateforme Intégrée IMAGIF – CNRS, Avenue de la Terrasse, Gif sur Yvette 91198, France

2 Centre de Génétique Moléculaire - CNRS, Avenue de la Terrasse, Gif sur Yvette 91198, France

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BMC Bioinformatics 2014, 15:198  doi:10.1186/1471-2105-15-198

Published: 18 June 2014

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.

Conclusion

CIRCUS allows fast and versatile analysis of genomic structural variants with Circos plots for users with limited coding skills.

Keywords:
Circos; Genomic structural variants; Genomic data visualization