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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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Documentation


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 citations

 (752)
library_books

Comparison of the Chinese bamboo partridge and red Junglefowl genome sequences highlights the importance of demography in genome evolution

2018
BMC Genomics
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 [], […]

library_books

Genome Sequencing and Analysis of the Peanut B Genome Progenitor (Arachis ipaensis)

2018
Front Plant Sci
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 […]

library_books

Comparative genomics of cocci shaped Sporosarcina strains with diverse spatial isolation

2018
BMC Genomics
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 […]

library_books

Whole genome de novo sequencing reveals unique genes that contributed to the adaptive evolution of the Mikado pheasant

2018
GigaScience
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 […]

library_books

Structural and functional dissection of differentially expressed tomato WRKY transcripts in host defense response against the vascular wilt pathogen (Fusarium oxysporum f. sp. lycopersici)

2018
PLoS One
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 […]

library_books

Comparative genomics of the wheat fungal pathogen Pyrenophora tritici repentis reveals chromosomal variations and genome plasticity

2018
BMC Genomics
PMCID: 5913888
PMID: 29685100
DOI: 10.1186/s12864-018-4680-3

[…] greater than 90% identity and greater than 5000 bp; segmental duplication genome coverage was determined using bedtools coverage v2.17.0., repeat coordinates were plotted to the m4 genome using circos version 0.69-3 []., final gene calls were performed for all isolates by the same workflow method (additional file ) for comparative analysis. ab-initio gene predictions were made […]


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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).
lshepard's avatar image No country

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..