Naquin Delphine, d'Aubenton-Carafa Yves, Thermes Claude, Silvain Maud
Plateforme Intégrée IMAGIF - CNRS, Avenue de la Terrasse, Gif sur Yvette 91198, France.
BMC Bioinformatics. 2014 Jun 18;15:198. doi: 10.1186/1471-2105-15-198.
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.
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.
CIRCUS allows fast and versatile analysis of genomic structural variants with Circos plots for users with limited coding skills.
大型基因组重排的检测，如大的插入缺失、重复或易位，现在通常通过下一代测序（NGS）方法来实现。最近，已经开发了几种工具来分析NGS数据，但如果没有额外的可视化步骤，生成的文件很难解释。Circos（《基因组研究》，19:1639 - 1645，2009年）是一个Perl脚本，是一个强大的可视化软件，需要设置大量带有众多参数的配置文件来处理。像RCircos（《BMC生物信息学》，14:244，2013年）或ggbio（《基因组生物学》，13:R77，2012年）这样的R包提供了将基因组数据显示为类似Circos圆形图的功能。然而，这些工具非常通用，缺乏过滤、格式化和调整特定输入基因组数据所需的功能。
我们实现了一个名为CIRCUS的R包来分析基因组结构变异。它生成Circos生成图形所需的数据和配置文件。只需要很少的R先决条件。有选项可用于处理异质数据、各种染色体数量和多尺度分析。
CIRCUS允许编码技能有限的用户使用Circos图快速且通用地分析基因组结构变异。
