Circos: An information aesthetic for comparative genomics

Abstract

We created a visualization tool called Circos to facilitate the identification and analysis of similarities and differences arising from comparisons of genomes. Our tool is effective in displaying variation in genome structure and, generally, any other kind of positional relationships between genomic intervals. Such data are routinely produced by sequence alignments, hybridization arrays, genome mapping, and genotyping studies. Circos uses a circular ideogram layout to facilitate the display of relationships between pairs of positions by the use of ribbons, which encode the position, size, and orientation of related genomic elements. Circos is capable of displaying data as scatter, line, and histogram plots, heat maps, tiles, connectors, and text. Bitmap or vector images can be created from GFF-style data inputs and hierarchical configuration files, which can be easily generated by automated tools, making Circos suitable for rapid deployment in data analysis and reporting pipelines.[Supplemental material is available online at http://www.genome.org. Circos is licensed under GPL and available at http:// mkweb.bcgsc.ca/circos. An interactive online version of Circos designed to visualize tabular data is available at http:// mkweb.bcgsc.ca/circos/tableviewer.]The continuing advances in speed, quality, and affordability of whole-genome analysis, including genome sequencing, have transitioned the comparative genomics field from the realm of comparing reference sequence assemblies to comparing assemblies of individual genomes. Whereas interspecies analysis leverages information about one species to further the understanding of biological mechanisms in another, comparative methods are now used to discover differences between individuals and the extent to which these differences affect response to the environment, such as susceptibility to disease and responsiveness to therapy.Our growing ability to collect enormous amounts of sequence information to support such studies is arguably outpacing the rate at which we devise new methods to store, process, analyze, and visualize these data. Any new approaches in data modeling and analysis need to be accompanied with corresponding innovations in the visualization of these data. To mitigate the inherent difficulties in detecting, filtering, and classifying patterns within large data sets, we require instructive and clear visualizations that (1) adapt to the density and dynamic range of the data, (2) maintain complexity and detail in the data, and (3) scale well without sacrificing clarity and specificity.

Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga

“…We annotated protein-coding genes by integrating evidence from RNA sequencing, ab initio predictions and comparison with UniProt. Most synteny and Ka/Ks (non-synonymous divergence/synonymous divergence) analyses were performed using the package MCScanX 29 and synteny plots were drawn using Circos 30 . alternates between a haploid phase (in which a single allele of each gene is present) and a diploid phase (in which the genes are present in two allelic versions arranged colinearly on homologous chromosomes).…”

Genome‐wide identification, expression profiling, and target gene analysis of microRNAs in the Onion thrips, Thrips tabaci Lindeman (Thysanoptera: Thripidae), vectors of tospoviruses (Bunyaviridae)

“…The synteny analysis of the T. tabaci miRNAs and their targets were performed by employing circos (Krzywinski et al., 2009). In brief, the Blast analysis was performed using T. tabaci miRNA sequences (known and novel) against F. occidentalis scaffolds (Approx.…”

“…Map of the Western Flower Thrips, F. occidentalis scaffolds linking T. tabaci mi RNA s and their putative targets prepared using Circos (Krzywinski et al., 2009). The outer circle represents the highlights of nine novel mi RNA represented in blue and 34 known mi RNA represented in red color.…”

“…The targets were further annotated against NCBI‐RefSeq invertebrate protein database and Gene Ontology (GO) terms were assigned (using Blast‐2‐GO) based on the annotation. The circos plot was generated using Circos (Krzywinski et al., 2009) to visualize the interaction between miRNAs and their targets.…”

Spatial pattern of adaptive and neutral genetic diversity across different biomes in the lesser anteater (Tamandua tetradactyla)

“…To envision the sharing of MHC alleles between biomes and individuals, Circus online tool (http://circos.ca/), a method of circular visualization of tables, was used (Krzywinski et al. 2009). Similarly, the evolutionary relationship between MHC alleles, biomes, and individuals was observed through a network taking the required number of mutations between alleles into account using a median‐joining algorithm (Bandelt et al.…”