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Martin Krzywinski
Project Description:
From the creator of Schemaball, Circos is designed for visualizing alignments, conservation and intra- and inter-chromosomal relationships within a genome, between genomes, or between any two or more sets of objects with a corresponding distance scale. Circos is written in Perl to be a flexible and extensible tool for the generation of publication-quality, circularly composited renditions of genomic data and related annotations.

Circos produces static images. Eventually, Circos will produce HTML image maps to make images interactive. Support exists for creating images with non-linear distance scales. The magnification level of genomic regions can be set independently and without cropping. Scale smoothing ensures that the magnification changes smoothly across the ideogram.

Circos is driven by an Apache-like configuration file and accepts data from flat files. It is very easy to plot, format and layer the data with Circos. A large variety of plot and feature parameters are customizable, helping you make the image that best communicates your data. 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.

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