Circos > Support > Getting Started
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Circos is coming to the EMBO NGS workshop in Tunis, Sept 15–25.

Circos Introduced in the New York Times

My first Circos infographic to be published in the New York Times introduces the idea of sequence similarity curves linking circularly composed ideograms.

Working with David Constantine, I illustrated the similarity between chromosome 1 of mouse, rhesus, chimp, and chicken to that of human.

One of the smaller panels in the infographic was subsequently used by the Alliance of Lupus Research in their Faces of Lupus II video.

Naming Names - Circos Engages in Political Mudslinging

Jonathan Corum of the New York Times prepared this infographic with Circos to show the extent and timing of the use of names of by presidential candidates in a series of debates. Each arrow represents one candidate refering to another, with the start of the arrow representing the time within the candidate's speech at which the reference was made.

The figure was part of a larger graphic that identified themes during the debate. Jonathan created an interactive version of this figure and discusses how he approached its design.

Getting Started

Don't know where to start? Start here!

Installation

First, download and install Circos. If you are a Windows user, please read the UNIX vs Windows tutorial, especially if you are not familiar with the command line.

If you run into problems, first make sure you have all necessary Perl modules. If you are certain that all modules are installed and functioning, use the Google Group to search for similar problems or post a question to the community.

Generate Example Image

To verify that Circos has been installed correctly, generate the example image. This is a complex image which will take about 1 minute to generate.

Example Circos image (600 x 600)
Example Circos image.

On UNIX (e.g. Linux), from the Circos installation directory

# UNIX
> cd example
> ./run
# batch file runs 'circos -conf ./circos.conf'
debuggroup summary 0.86s parsing karyotype and organizing ideograms
debuggroup summary 1.08s applying global and local scaling
debuggroup summary 1.15s allocating image, colors and brushes
debuggroup summary 7.19s drawing highlights and ideograms
debuggroup summary 8.94s processing links
debuggroup summary 13.31s processing data tracks
Processing text track - this might take a while
debuggroup summary 68.75s generating output
created image at ./circos.png
created image at ./circos.svg
# look at circos.png

On Windows, from the Circos installation directory

# Windows
> cd example
> perl ..\bin\circos -conf circos.conf

Tutorials and Documentation

Circos documentation is available as a series of online tutorials which describe all of the features in Circos in a logical progression.

quick start

If you are impatient and want the shortest route to creating an image, read the Quick Guide tutorials. This is a series of 8 tutorials that show you how to build up an image from scratch, using data displayed on the human genome chromosomes.

Circos quick start tutorials (800 x 800)
Circos quick start tutorials quickly show you how to build up an image from scratch.

best practices

It's not always clear how to proceed when you're starting out. Refer to the Circos Best Practices guide for tips to make your configuration modular and streamlined.

legacy configuration files

Many users experience issues caused by using new versions of Circos with old configuration files. If you are getting started, always use the newest version of Circos.

extended tutorials

The data and configuration files for all online tutorials can be downloaded as a separate package. If one of the tutorials can act as a template for your image, use it as a starting point.

support

Direct your Circos questions (installation, configuration, best practices) to the Google Group.

Using Circos in Publications

If you are considering using Circos for a figure in a publication or magazine, look through published images for inspiration.

  • Circos can be used to visualize genomic data
  • Circos can be used to visualize any other data, such as debates, bus schedules, relationships, social network, network traffic, and things we haven't though of
  • Circos requires Perl to run
  • Circos does not have a user interface—it is controlled through a plain-text configuration file
  • Circos can be easily automated
  • Circos can generate SVG files which you can post-process in Illustrator or Inkscape

If you are close to publication, I am happy to help you design and/or refine your image. I've done it many times before—drop me a line and we'll get started.

Using Circos as Art

If you like things round, and distrust things square, Circos can be a platform for visual expression.

It has been used artistically before, perhaps most prominently in the David Cronenberg Chromosomes exhibit, where I collaborated with Volumina to give the book and exhibit a scientific feel.