Circos

Visualize comparative genomic data such as alignments, conservation, homology, synteny and other positional n-tuples in an attractive and informative circular layout.

Project Description

Circos is designed for visualizing genomic data such as alignments, conservation, and generalized 2D data, such as line, scatter, heatmap and histogram plots.

The creation of Circos was motivated by a need to visualize intra- and inter-chromosomal relationships within one or more genomes, or between any two or more sets of objects with a corresponding distance scale. Circos is similar to chromowheel and, to a lesser extent, genopix.

Circos uses a circular composition of ideograms to mitigate the fact that some data, like combinations of intra- and inter-chromosomal relationships (alignments, duplications, assembly paired-ends, etc) are very difficult to organize when the underlying ideograms (or contigs) are arranged as lines. In many cases, it is impossible to keep the relationship lines from crossing other structures and this deteriorates the effectiveness of the graphic.

Specific features are included to help viewing data on the genome. The genome is a large structure with localized regions of interest, frequently separated by large oceans of uninteresting sequence. To help visualize data in this context, Circos can create images with variable axis scaling, permitting local magnification of genomic regions to be controlled without cropping. Scale smoothing ensures that the magnification level changes smoothly. In combination with axis breaks and custom ideogram order, the final image can be easily tuned to offer the clearest illustration of your data.

All aspects of the output image are tunable, making Circos a flexible and extensible tool for the generation of publication-quality, circularly composited renditions of genomic data and related annotations.

Circos is written in Perl and produces bitmap (PNG) and vector (SVG) images using plain text configuration and input files.