Circos

Circos visualizes positional relationships and structural variation in genomic and other positional datasets using a circular ideogram layout.

Key Features:

• Circular ideogram layout: Displays positional relationships between genomic intervals on a circular ideogram to represent chromosomal positions around a circle.
• Ribbons encoding links: Represents connections between pairs of positions using ribbons that encode the position, size, and orientation of related genomic elements.
• Multiple plot types: Supports scatter plots, line graphs, histograms, heat maps, tiles, connectors, and text annotations for layered data representation.
• Input formats: Accepts GFF-style data inputs for specifying genomic intervals and features.
• Output formats: Produces both bitmap and vector images for publication-quality figures.
• Data source compatibility: Handles data from sequence alignments, hybridization arrays, genome mapping, and genotyping studies as well as other positional datasets.
• Hierarchical configuration files: Uses hierarchical configuration files that can be automatically generated by other tools for integration into analysis workflows.

Scientific Applications:

• Comparative genomics: Identification and analysis of genomic similarities and differences across genomes using comparative visualizations.
• Structural variation visualization: Visualization of structural variants and rearrangements by illustrating connections and orientations between genomic loci.
• Multi-assay integration: Integration and visual comparison of data from sequence alignments, hybridization arrays, genome mapping, and genotyping studies.
• Non-genomic positional analyses: Visualization of positional relationships in diverse non-genomic datasets that can be represented on a circular layout.

Methodology:

Generates circular ideograms and ribbons that encode position, size, and orientation from GFF-style inputs, renders scatter/line/histogram/heat map/tile/connector/text tracks, uses hierarchical configuration files, and outputs bitmap and vector images.