Circos specifications

Information


Unique identifier OMICS_00932
Name Circos
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Windows
Programming languages Perl
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.69-6
Stability Stable
Maintained Yes

Download


Versioning


Add your version

Documentation


Maintainer


  • person_outline Martin Krzywinski <>

Additional information


Web app : http://mkweb.bcgsc.ca/tableviewer/visualize/; Tutorials : http://circos.ca/documentation/tutorials/

Information


Unique identifier OMICS_00932
Name Circos
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Martin Krzywinski <>

Additional information


Web app : http://mkweb.bcgsc.ca/tableviewer/visualize/; Tutorials : http://circos.ca/documentation/tutorials/

Circos article

Circos citations

 (16)
2017
PMCID: 5742254

[…] primer length were designed from the extracted sequences by using primer3 software (untergasser et al., 2012). the circular plots were constructed using standalone version of circos software (http://circos.ca/) developed at the genome sciences centre in vancouver, canada (krzywinski et al., 2009). the insertion and deletion densities are plotted at a window size of 100 kb., primer pairs […]

2017
PMCID: 5850475

[…] on the south green platform https://github.com/southgreenplatform (last accessed may 29, 2017) in the scaffremodler toolbox (martin et al. 2016). discordant read clusters were visualized using circos software (krzywinski et al. 2009)., primer pairs were designed at the boundaries of the identified rearrangement breakpoint in the pt-ba-00267 accession. primers 1lf […]

2017
PMCID: 5217421

[…] changes (alter amino acid sequence) were identified with the effect predictor of snpeff v3.1 h [60]. the distribution of snps and indels on each cucumber chromosomes was visualized using circos [61]., total rna was extracted using rneasy mini kit (qiagen, germany) following the manufacturer’s instructions and checked for a rin number to inspect rna integrity by an agilent bioanalyzer […]

2016
PMCID: 4969343

[…] 8; gap existence cost, 5; gap elongation cost, 2; and nucleotide match/mismatch scores, 1/−2. microsyntenic blocks were visualized using the web-based genome synteny viewer (revanna et al. 2011) and circos (krzywinski et al. 2009)., primers for molecular markers amplification were designed based on bess with the use of primer3 plus software (untergasser et al. 2007). to identify polymorphic […]

2016
PMCID: 4841963

[…] their region in the transcripts (orfs, 3′-utr and 5′-utr) were detected using the bedtools utilities [122]. the representation of the ssrs distribution along the eggplant genome was performed with circos software. one ssr per eggplant chromosome was selected in order to validate them in the s. incanum and s. aethiopicum sequenced genotypes., all selected ssrs for validation were checked via […]

Circos institution(s)
Canada’s Michael Smith Genome Sciences Center, Vancouver, BC, Canada; British Columbia Cancer Research Center, British Columbia Cancer Agency, Vancouver, BC, Canada
Circos funding source(s)
Supported by Genome Canada and Genome British Columbia, and the National Cancer Institute/Terry Fox Foundation.

Circos reviews

 (2)
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Dr Nick

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Desktop
A daunting tool to learn if you're not familiar with python scripting, but also one that has near limitless customization to produce incredibly crisp graphics that are immensely information dense (I've seen a few manuscripts where a Circos plot was the authors' ONLY figure). While a lot of stripped down GUI tools exist to capture the core capabilities of this program, it is more than worth your while to spend a few weeks running through all of the tutorials and customizing your plots for any number of applications (we use it a lot for display microRNA target relationships in grouped fashion with expression historgrams as an added layer).

lshepard

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Desktop
Great tool to show genomic data including relationships among biological conditions or cross-sequencing (eg.: RNA-seq with WGBS) correlations etc..