Circos data visualization

Circos is a Perl language based software package for visualizing similarities and differences of genome structure and positional relationships between genomic intervals. Running Circos requires extra data processing procedures to prepare plot data files and configure files from datasets, which limits its capability of integrating directly with other software tools such as R.

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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.

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Advances in high-resolution mass spectrometry facilitate the identification of hundreds of metabolites, thousands of proteins and their post-translational modifications. This remarkable progress poses a challenge to data analysis and visualization, requiring methods to reduce dimensionality and represent the data in a compact way.

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I am very pleased to have had an opportunity to write this book on Circos. It is a wonderful program that is innovative and applicable to many fields. Oddly, my first experience with Circos, after seeing an article on the cover of a 2007 American Scientist magazine, was to dismiss the diagrams as they were too complex. Yet, I found them to be beautiful and fascinating. I reflected on how the diagrams could be used to tell a story. Several months later I found myself using the program for a project, Visualizing Transitions into the Workforce.

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