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Circos at the EMBO NGS workshop in Tunis, Sept 15–25.

The terrifying dinosaur corn genome

Amblin Entertainment and Legendary Pictures, the studios that produced Jurrasic World, try to inject genome science into the movie. Unfortunately, since we don't quite know how to construct viable genomes of extinct species, much less grow the creatures themselves, we don't know whether the depiction of the science is right. Perhaps theirs is exactly what a genome lab would look like in a dino-building facility.

But, we can get fewer things wrong. In the Creation Lab companion website, a Circos image is used to illustrate a triceratops genome.

Unfortunately, this is an image of the B73 Maize reference genome (B73 RefGen_v1), as published in Nature's The B73 Maize Genome: Complexity, Diversity, and Dynamics.

Schnable PS Ware D Fulton RS et al. 2009 The B73 maize genome: complexity, diversity, and dynamics Science 326 (5956) 1112-1115

Using News Reports to Track Wildlife Black Markets

THE INTERNATIONAL BLACK market in wildlife—alive or dead—is notoriously difficult to track. Hunters and smugglers don’t report their take for the same reasons that drug dealers don’t report profits to the IRS. But if you could actually track those networks, maybe you could do something about them. That’s what sent Nikkita Patel, a veterinary epidemiologist at the University of Pennsylvania, to an unusual source of data on the illegal wildlife trade: the news.


The image shows the illegal global rhinoceros trade network before (top) and after (bottom) a hypothetical targeted disruption. Created with Circos online table viewer.

Circos Maps America’s Restless Interstate Migration Without a Map

Wired has a writeup about migration patterns within the US that shows the data using d3.js chord diagrams, modeled after how Circos shows tabular data.

Circos reaches 500 literature citations

In October 2013 Circos reached a milestone - 500 citations in peer-reviewed literature.

To celebrate, I've made a commemorative poster that features over 400 Circos images from the literature.

citation list | image gallery | press highlights

Circos for R

Zhang et al. implement Circos in R.

Same round shape you expect. And now, in everyone's favourite open source statistics and data analysis environment.

CRAN RCircos package

Zhang H, Meltzer P, Davis S 2013 RCircos: an R package for Circos 2D track plots BMC Bioinformatics 14:244.

Circos Interchange Diagrams — Networks and Flow

Zeng et al. introduce a new type of visualization based on Circos, the interchange diagram, in their paper Visualizing Interchange Patterns in Massive Movement Data.

The design is applied to displaying movement data, such as daily trips made by passengers in a city. By incorporating interactivity, this visualization method is helpful to understand interchange patterns at different spatial (between trains, between cities) and time scales (different times of day).

Circos has been used for urban planning before. The town of Caceres in Spain has used Circos to communicate their urban planning strategy.

project website

Zeng W, Fu C-W, Arisona SM et al. 2013 Visualizing Interchange Patterns in Massive Movement Data Computer Graphics Forum 32:271-280

Circos connects to the connectome

Methods to visualize the connectome are reviewed in Craddock et al — Circos is one of them.

Craddock RC, Jbabdi S, Yan C-G et al. 2013 Imaging human connectomes at the macroscale Nat Meth 10:524-539.

The use of Circos for showing the connectome was introduced by Irimia et al. in Circular representation of human cortical networks for subject and population-level connectomic visualization.

A good layman description of the work can be found at the neurosceptic blog.

Irimia A, Chambers MC, Torgerson CM et al. 2012 Circular representation of human cortical networks for subject and population-level connectomic visualization NeuroImage, Irimia A, Chambers MC, Torgerson CM et al. 2012 Patient-tailored connectomics visualization for the assessment of white matter atrophy in traumatic brain injury Frontiers in Neurology 3

Circos is the Method for Visualizing Translocations

Genomic rearrangements can cause disease and are implicated in many cancers. Being able to see the patterns in these changes across samples and patients is important.

In the review article End-joining, Translocations and Cancer, Bunting and Nussenzweig demonstrate how compositing the genome circularly adds value and clarity to the presentation.

Bunting SF, Nussenzweig A 2013 End-joining, translocations and cancer Nat Rev Cancer

From Degree to Job — Circos Visualizes Workforce Transitions

Finding the relationship between a student's major and career field is the topic of "Measuring Transitions Into The Workforce As A Form Of Accountability". The diagrams connect the flow of students from one of 17 fields of study (left) to job sectors (right).

Schenk TL, Jr. 2011 Measuring Transitions into the Workforce as a Form of Accountability SSRN eLibrary ID 1831967

Satyan L Devadoss from Williams College performed a similar analysis of Impact of Major on Career Path for 15600 Williams College Alums.

Circos tackles the connectome

Irimia et al. introduce circular representation of cortical networks in Circular representation of human cortical networks for subject and population-level connectomic visualization. The scalability of this circular visualization approach is demonstrated by lucid aggregate visualizations using cortical networks of 50 individuals.

The UCLA group also used the circular connectome visualization to assess differences in brain injury in patients Patient-tailored connectomics visualization for the assessment of white matter atrophy in traumatic brain injury in Frontiers in Neurotrauma.

A good layman description of the work can be found at the neurosceptic blog.

Irimia A, Chambers MC, Torgerson CM et al. 2012 Circular representation of human cortical networks for subject and population-level connectomic visualization NeuroImage, Irimia A, Chambers MC, Torgerson CM et al. 2012 Patient-tailored connectomics visualization for the assessment of white matter atrophy in traumatic brain injury Frontiers in Neurology 3

Hemolytic–Uremic Syndrome Outbreak

Rasko et al. use Circos to show how the E. coli strain implicated in the German outbreak of hemolytic-uremic syndrome varies from other strains in their New England Journal of Medicine paper, where they find that "the genome of the German outbreak strain can be distinguished from those of other O104:H4 strains because it contains a prophage encoding Shiga toxin 2 and a distinct set of additional virulence and antibiotic-resistance factors."

NEJM created an animation that explains the visualizations. The paper was blogged by Pacific Biosciences.

Rasko DA, Webster DR, Sahl JW et al. 2011 Origins of the E. coli Strain Causing an Outbreak of Hemolytic-Uremic Syndrome in Germany The New England journal of medicine published ahead of print:-.

Circos Maps Cancer Landscapes

Nature features an article by Heidi Ledford, The Cancer Genome Challenge, which discusses the progress and challenges of identifying structural variation signatures in cancer genomes.

Circos images are used throughout the piece, taken from the COSMIC project (Catalogue of Somatic Mutations in Cancer).

Ledford H 2010 Big science: The cancer genome challenge Nature 464 (7291) 972-974.

Linux kernel exploration

Răzvan Musăloiu-E. explored the Linux file system and used Circos to relate the systems (disk-based, optical mediums, flash-based, network-based, cluster-based, memory-based, ancient) to kernel symbols.

Circular Worle

Jonathan Feinberg (IBM) created this perfectly circular wordle for me, using content from the Circos site.

As far as I know, this is the only circular wordle.

Circos Citation Themes

A wordle created from the words of the over 100 scientific articles that cite Circos.

All Your Genes Are Belong To Us

Remembering one of the most viral internet memes.

Circos is catching on, too.

Circos at VIZBI 2011

Circos was one of the community visualization tool tutorials at VIZBI 2011, at the Broad Institute in Boston.

Circos Helps with Urban Planning

The town of Caceres, Spain, a UNESCO World Heritage Site, used Circos to illustrate the relationships between businesses in their urban planning strategy.

Hive Plots - Linear Layout for Network Visualization

Visualizing large networks is hard. Nobody wants to see another hairball, but you want to show your data.

What do you do?

Try our new linear layout for network visualization, introducing the hive plot. This plot takes a fresh approach to drawing networks. It scales well, shows topology, and makes the network layout based on meaningful properties.

Power of Round

Circular data tracks naturally support display of information at various resolutions.

Compared to a track at a radius r, a pixel in a track at r/4 will span a region 4x larger. Tracks in the interior of the figure are therefore useful to display low-resolution or summary information.

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.

NYT Article - Mapping the Epigenome

In collaboration with Jonathan Corum from the NYT, Martin Krzywinski created an illustration of data showing methylation on chromosome 22 in a variety of tissues.

The illustration accompanies the article Now: The Rest of the Genome, by Carl Zimmer.

Download Circos, Tutorials and Tools

Distribution packs

Circos is distribted in three independent archives.

To do anything, you'll need the Circos code distribution, which contains the main code, fonts, global configuration and an example. Tutorials are no longer included in this file.

To learn how to use circos, download the tutorials, which contain many examples to demonstrate Circos' features. These tutorials are also available online.

Several, utility add-on scripts are available, such as for bundling links. These are not necessary for Circos, but helpful in carrying out common data reduction and analysis tasks. Tools are described in the Tools Tutorial.

Bug reports

Please direct bug reports, comments and questions to the Circos Google group.

To help resolve the problem faster, send me your conf/data files. Do not forget to include all the files, including karyotype.


file version size date comment
circos-0.68-pre1.tgz 0.68 27,675,150 Tue Apr 7 13:59:20 2015 This is a pre-release candidate.
circos-0.68-pre0.tgz 0.68 27,675,147 Thu Mar 26 11:48:31 2015 This is a pre-release candidate.
circos-0.67-7.tgz 0.67 27,671,220 Mon Mar 16 17:30:00 2015 circos-0.67-7.tgz is a bug release.
circos-0.67-6.tgz 0.67 27,671,036 Fri Feb 27 12:14:08 2015 circos-0.67-6.tgz is a bug release.
circos-0.67-5.tgz 0.67 27,671,014 Mon Jan 19 13:45:35 2015 circos-0.67-5.tgz is a bug release.
circos-0.67-4.tgz 0.67 28,022,579 Thu Nov 27 12:30:04 2014 circos-0.67-4.tgz is a bug release.
circos-0.67-3.tgz 0.67 28,024,964 Tue Nov 25 16:45:42 2014 circos-0.67-3.tgz is a bug release.
circos-0.67-2.tgz 0.67 28,015,396 Tue Nov 18 17:08:47 2014 circos-0.67-2.tgz is a bug release.
circos-0.67-1.tgz 0.67 28,014,985 Mon Oct 6 14:57:23 2014 circos-0.67-1.tgz is a bug release.
circos-0.67.tgz 0.67 28,151,712 Thu Oct 2 12:24:25 2014
circos-0.67-pre7.tgz 0.67 26,565,493 Wed Sep 17 18:02:01 2014 This is a pre-release candidate.
circos-0.67-pre6.tgz 0.67 26,419,363 Wed Sep 3 16:53:07 2014 This is a pre-release candidate.
circos-0.67-pre5.tgz 0.67 26,418,805 Mon Jun 16 12:12:29 2014 This is a pre-release candidate.
circos-0.67-pre4.tgz 0.67 26,725,778 Tue Jun 3 17:36:54 2014 This is a pre-release candidate.
circos-0.67-pre3.tgz 0.67 26,775,513 Fri May 2 16:15:27 2014 This is a pre-release candidate.
circos-0.67-pre2.tgz 0.67 26,775,745 Thu May 1 21:05:52 2014 This is a pre-release candidate.
circos-0.67-pre1.tgz 0.67 26,775,733 Wed Apr 30 15:12:24 2014 This is a pre-release candidate.
circos-0.67-pre0.tgz 0.67 24,814,333 Wed Apr 16 21:58:15 2014 This is a pre-release candidate.
circos-0.66.tgz 0.66 24,811,477 Mon Apr 7 16:43:49 2014
circos-0.65-pre7.tgz 0.65 26,416,287 Thu Mar 27 17:37:02 2014 This is a pre-release candidate.
circos-0.65-pre6.tgz 0.65 26,416,162 Thu Mar 6 11:39:43 2014 This is a pre-release candidate.
circos-0.65-pre5.tgz 0.65 26,778,242 Thu Oct 10 15:41:15 2013 This is a pre-release candidate.
circos-0.65-pre4.tgz 0.65 26,775,836 Wed Aug 7 17:35:01 2013 This is a pre-release candidate.
circos-0.65-pre3.tgz 0.65 26,766,284 Thu Jun 13 17:47:42 2013 This is a pre-release candidate.
circos-0.65-pre2.tgz 0.65 26,766,130 Thu Jun 13 15:30:09 2013 This is a pre-release candidate.
circos-0.65-pre1.tgz 0.65 24,227,779 Fri Jun 7 16:55:37 2013 This is a pre-release candidate.
circos-0.65-pre0.tgz 0.65 24,105,067 Tue May 14 16:39:40 2013 This is a pre-release candidate.
circos-0.64.tgz 0.64 24,103,895 Fri May 3 17:49:46 2013
circos-0.64-pre1.tgz 0.64 24,102,961 Fri Apr 19 17:13:26 2013 This is a pre-release candidate.
circos-0.64-pre0.tgz 0.64 23,989,302 Fri Mar 15 19:18:11 2013 This is a pre-release candidate.
circos-0.63-4.tgz 0.63 23,987,760 Fri Feb 15 16:03:07 2013 circos-0.63-4.tgz is a bug release.
circos-0.63-3.tgz 0.63 23,986,105 Wed Feb 13 14:08:45 2013 circos-0.63-3.tgz is a bug release.
circos-0.63-2.tgz 0.63 23,985,859 Tue Feb 12 15:40:02 2013 circos-0.63-2.tgz is a bug release.
circos-0.63-1.tgz 0.63 24,047,989 Thu Feb 7 14:39:41 2013 circos-0.63-1.tgz is a bug release.
circos-0.63.tgz 0.63 24,047,810 Mon Feb 4 17:19:48 2013
circos-0.62-1.tgz 0.62 23,776,624 Tue Jul 3 12:59:00 2012 circos-0.62-1.tgz is a bug release.
circos-0.62.tgz 0.62 21,905,722 Mon Jun 25 15:30:13 2012
circos-0.61.tgz 0.61 11,721,669 Mon Jun 4 18:01:25 2012
circos-0.60.tgz 0.60 12,746,160 Tue May 8 05:57:19 2012
circos-0.56-1.tgz 0.56 5,869 Tue Feb 7 18:44:49 2012 circos-0.56-1.tgz is a bug release.
circos-0.56.tgz 0.56 8,680,766 Mon Feb 6 13:52:56 2012
circos-0.56-pre4.tgz 0.56 8,778,743 Sat Feb 4 18:27:31 2012 This is a pre-release candidate.
circos-0.56-pre3.tgz 0.56 8,776,310 Tue Jan 31 15:51:36 2012 This is a pre-release candidate.
circos-0.56-pre2.tgz 0.56 10,027,617 Tue Nov 1 17:15:19 2011 This is a pre-release candidate.
circos-0.56-pre1.tgz 0.56 10,026,887 Fri Oct 28 16:44:40 2011 This is a pre-release candidate.
circos-0.56-pre0.tgz 0.56 10,025,575 Sat Sep 10 17:43:13 2011 This is a pre-release candidate.
circos-0.55.tgz 0.55 9,808,083 Tue Aug 9 12:44:25 2011
circos-0.55-pre2.tgz 0.55 11,910,581 Sat Jul 9 11:21:58 2011 This is a pre-release candidate.
circos-0.55-pre1.tgz 0.55 11,910,218 Thu Jun 16 16:34:30 2011 This is a pre-release candidate.
circos-0.55-pre0.tgz 0.55 11,937,893 Sun Jun 12 22:22:14 2011 This is a pre-release candidate.
circos-0.54-1.tar.gz 0.54 129,786 Wed Apr 13 16:12:30 2011 circos-0.54-1.tar.gz is a bug release.
circos-0.54.tar.gz 0.54 63,241,152 Tue Mar 29 14:35:57 2011
circos-0.53.tgz 0.53 50,501,105 Mon Mar 14 16:29:48 2011
circos-0.52-4.tgz 0.52 67,537 Wed Feb 9 15:18:47 2011 circos-0.52-4.tgz is a bug release.
circos-0.52-3.tgz 0.52 66,262 Tue Jan 11 16:37:05 2011 circos-0.52-3.tgz is a bug release.
circos-0.52-2.tgz 0.52 66,173 Tue Sep 21 15:49:32 2010 circos-0.52-2.tgz is a bug release.
circos-0.52-1.tgz 0.52 65,628 Fri Sep 3 11:32:54 2010 circos-0.52-1.tgz is a bug release.
circos-0.52.tgz 0.52 43,523,958 Tue Nov 24 17:06:54 2009
circos-0.51-1.tgz 0.51 80,694 Wed Jul 8 15:02:27 2009 circos-0.51-1.tgz is a bug release.
circos-0.51.tgz 0.51 43,531,650 Tue Jul 7 10:13:23 2009
circos-0.50.tgz 0.50 43,239,234 Thu Jun 25 16:28:07 2009
circos-0.48-1.tgz 0.48 53,782 Wed Jun 17 10:51:54 2009 circos-0.48-1.tgz is a bug release.
circos-0.49.tgz 0.49 73,468,067 Fri Jan 30 15:36:13 2009
circos-0.48.tgz 0.48 60,165,323 Tue Oct 21 10:43:48 2008
circos-0.47.tgz 0.47 52,984,724 Wed Oct 1 16:24:55 2008
circos-0.46.tgz 0.46 51,631,977 Mon Jul 28 10:21:10 2008
circos-0.45-1.tgz 0.45 47,527 Mon Jun 30 14:55:00 2008 circos-0.45-1.tgz is a bug release.
circos-0.45.tgz 0.45 46,994,783 Wed Jun 25 13:48:39 2008
circos-0.44.tgz 0.44 47,038,048 Tue Jun 24 17:57:46 2008
circos-0.43.tgz 0.43 47,041,650 Mon May 12 16:33:33 2008
circos-0.42.tgz 0.42 46,073,900 Mon Apr 28 14:23:00 2008
circos-0.41.tgz 0.41 46,069,712 Wed Apr 23 16:06:56 2008
circos-0.40.tgz 0.40 46,113,934 Mon Apr 21 16:28:12 2008
circos-0.39.tgz 0.39 45,583,858 Tue Apr 15 11:42:01 2008
circos-0.38.tgz 0.38 45,400,582 Wed Apr 9 14:38:03 2008
circos-0.37.tgz 0.37 42,909,432 Wed Feb 27 14:04:34 2008
circos-0.36.tgz 0.36 37,876,802 Thu Jan 3 13:50:46 2008
circos-0.35.tgz 0.35 33,562,094 Mon Dec 24 17:26:23 2007
circos-0.34.tgz 0.34 32,739,695 Sat Dec 22 16:46:20 2007
circos-0.33.tgz 0.33 28,236,518 Tue Dec 4 17:50:16 2007
circos-0.32.tgz 0.32 24,127,638 Tue Nov 20 17:31:59 2007
circos-0.31.tgz 0.31 14,170,380 Sun Oct 28 14:37:29 2007
circos-0.22.tgz 0.22 3,069,083 Wed Jan 24 14:00:00 2007
circos-0.21.tgz 0.21 91,764 Tue May 24 16:31:09 2005
circos-0.2.tgz 0.20 92,006 Tue May 24 01:37:49 2005