Circos protocols

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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

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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


Additional information


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

Publication for Circos

Circos in pipelines

 (145)
2018
PMCID: 5748942
PMID: 29291727
DOI: 10.1186/s12864-017-4249-6

[…] a sliding window of 5 kb (snp absolute frequency divided by the length of the window). to visualize if there were heterogeneous snp-dense regions in the genome, we visualized these densities with circos (v0.69) []. we used snpsift (v4.2) [], a vcf-manipulation tool, to extract all the genes contained between the snp-densest regions., snpeff was used to annotate variants of the local strains […]

2018
PMCID: 5755439
PMID: 29304732
DOI: 10.1186/s12864-017-4421-z

[…] scaffolds were mapped only if they contain at least two snps. the graphical presentations of the genomic features and the physical map integrated with genetic linkage map were generated by using circos 0.69 []., the 115 monokaryotic individuals were first crossed with the two parental lines h6pa and h6pb. all mating tests were made on pda plates. cultures were grown at 25 °c for 10 days. […]

2018
PMCID: 5821079
PMID: 29463655
DOI: 10.1128/mBio.01650-17

[…] clustering was performed on average rlog-transformed values for each gene and condition. the optimal number of clusters was defined using the elbow plot method and circular heatmaps drawn using circos (). go enrichment analysis was carried out with the enrichgo function in the r package clusterprofiler version 3.4.4 () by the molecular function ontology method and the holm method to correct […]

2018
PMCID: 5825990
PMID: 29515596
DOI: 10.3389/fpls.2018.00021

[…] sites where at least one variety differs from the other five using in-house scripts (supplementary table , ). relative snp densities were determined using a 100 kb window and plotted using the circos plotting tool (krzywinski et al., )., predicted proteome sequences from citrus clementine, solanum lycopersicum, fragaria vesca, malus domestica, arabidopsis thaliana, vitis vinifera, p. […]

2018
PMCID: 5826181
PMID: 29515524
DOI: 10.3389/fmicb.2018.00079

[…] (katoh and standley, ). the concatenated alignment was used for the reconstruction of the species tree using fasttree 2.1.9 with double precision (price et al., ). circular plots were drawn using circos version 0.69 (krzywinski et al., ), whereas other plots were made with r (r core team, )., all genomes were annotated using ghostkoala (kanehisa et al., ) and interproscan version 5.23–62.0 […]


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Circos in publications

 (704)
PMCID: 5941490
PMID: 29739321
DOI: 10.1186/s12864-018-4711-0

[…] bases, pairwise nucleotide diversity, and gc content for non-overlapping 100 kb sliding windows from the alignable sequences using perl scripts. results from sliding windows were visualized with circos []., we circumscribed gene families from the annotated genomes of gallus gallus, bambusicola thoracicus, coturnix japonica, meleagris gallopavo, and colinus virginianus using orthomcl [], […]

PMCID: 5943715
PMID: 29774047
DOI: 10.3389/fpls.2018.00604

[…] (tamura et al., )., syntenic blocks between the genomes of a. ipaensis and other plants were identified using the mcscanx with default parameters (wang et al., ) and visualized on the genome using circos (krzywinski et al., ). genomic sequences were first aligned annotated genes based on amino acid sequence using promer package of mummer (version 3.22) (delcher et al., ). whole genome dot […]

PMCID: 5941149
PMID: 29722814
DOI: 10.1093/gigascience/giy044

[…] were investigated and visualized. the structural variants among the species were further reported using the “show-diff” utility in mummer. the chord diagrams of the alignment were generated using circos []., first, repeatmasker (version 4.0.5; parameter: “-species chicken”), including rmblastn (version 2.2.23+) as the search engine, repbase (version 20140131), and rm database (version […]

PMCID: 5930826
PMID: 29716534
DOI: 10.1186/s12864-018-4635-8

[…] sites that have a phred-like quality value (qv) score of 50 or greater were presented in this study []. to visualize the methylomes, all modifications were plotted against each genome using circos (v.0.69) []., contigs for each of the draft genomes (illumina sequenced strains and s. ureae str. dsm 2281) were re-ordered using the program mauve (v2.4.0) [], with the closest related strain […]

PMCID: 5927432
PMID: 29709017
DOI: 10.1371/journal.pone.0193922

[…] providing a comparative evaluation to identify the similarities and differences across the wrky members having homologous and/or orthologous relationship with the solywrky33 and solywrky37 using the circos visualization http://circos.ca/ []. the circos results were determined based on the percentage identity matrices obtained through phylogenetic clustering using clustal w at 0 percent cut-off […]


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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).
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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..