Circos pipeline

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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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/

Publication for Circos

Circos IN pipelines

 (49)
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 [51]., 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: 5827201
PMID: 29483551
DOI: 10.1038/s41598-018-21844-6

[…] a paired t-test and analysis of treatment status was performed with a two-sample t-test. all p values are two-tailed. tables were generated using microsoft excel; figures were generated using r, circos18 and inkscape., the cgci non-hodgkin lymphoma – diffuse large b-cell lymphoma project dataset is available through dbgap (www.ncbi.nlm.nih.gov/gap); accession number phs000532.v6.p2., , […]

2018
PMCID: 5877630
PMID: 29517986
DOI: 10.3390/ijms19030769

[…] determined according to the genome annotation files downloaded from the cottongen website (available online: https://www.cottongen.org). the sweet genes were mapped using mapinspect software [54] or circos (version 0.69) software [55]. tandem duplications were analyzed on the basis of the same or neighboring chromosomal regions [56]. homologous genes including paralogous and orthologous genes […]

2017
PMCID: 5417524
PMID: 28472185
DOI: 10.1371/journal.pone.0176909

[…] putative mas (please refer to s4 file for details) were predicted in coding region sequences. the exact locations of these new putative mas of hervs in the human chromosomes have been described with circos [75] software and shown in fig 1., the angles of the dark red lines represent the exact positions of new putative mas of hervs in the human chromosomes. the length of the line is proportional […]

2017
PMCID: 5469757
PMID: 28611446
DOI: 10.1038/s41598-017-03445-x

[…] species based on the order of orthologues from the orthomcl output with default values. b. canis contigs were arranged according to the syntenic relationship to b. bovis with ‘orderchr’ execution in circos utilities. the graphical representation was made with circos113. whole genome phylogeny was based on the 975 identified orthomcl-orthologues shared among apicomplexan species. […]

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 review

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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).