Circleator protocols

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Circleator specifications

Information


Unique identifier OMICS_05206
Name Circleator
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data Some reference sequence(s) and annotation.
Output data Some publication-quality scalable vector graphics.
Operating system Unix/Linux
Programming languages Perl
License Artistic License version 2.0
Computer skills Advanced
Version 1.01
Stability Stable
Requirements
BioPerl, JSON, Log::Log4perl, SVG, Text::CSV, Vcf, Apache Batik, samtools, vcftools
Maintained Yes

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Versioning


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Documentation


Maintainer


  • person_outline Jonathan Crabtree <>

Additional information


http://jonathancrabtree.github.io/Circleator/documentation.html

Publication for Circleator

Circleator in pipelines

 (2)
2017
PMCID: 5337907
PMID: 28262711
DOI: 10.1038/srep43555

[…] neighbour-joining method with jukes-cantor and 1,000 bootstrap replicates as the nucleotide substitution model and method to test phylogeny, respectively. a circular plot was constructed using the circleator tool to demonstrate the locations of snps among the three isolates in the present study. pair-wise average nucleotide identity (ani) based on blast was calculated for the genome sequence […]

2015
PMCID: 4453556
PMID: 25873374
DOI: 10.1128/mBio.00231-15

[…] to reference microbial and viral databases are detailed in in the supplemental material. circular genome plots with mapped transcripts and metagenomic coverage were generated using the program circleator (). lda effect size (lefse) analysis was used to identify discriminant species and cogs across comparison transcriptome groups ()., mapped reads were totaled using htseq-count () […]


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Circleator in publications

 (5)
PMCID: 5609408
PMID: 28935729
DOI: 10.1128/genomeA.00923-17

[…] assembler version 1.2, and celera assembler version 8.2. the assemblers were run at default. assemblies were assessed for inconsistencies and misassembly using nucmer whole-genome alignments and circleator plots (gc skew). the genome was assembled into a single contig with average read coverage of 205-fold. the gc content was 28.62%. the contig was circularized using circlator version 1.5.1. […]

PMCID: 5597755
PMID: 28912314
DOI: 10.1128/genomeA.00897-17

[…] assemblers with default parameters for bacterial genome assembly. the resulting assemblies were assessed for inconsistencies and misassembly using nucmer version 3.0 whole-genome alignments () and circleator plots (gc-skew) (). canu version 1.2 () generated a single contig representing the chromosome, which was polished using quiver (smrt analysis┬áversion 2.3.0) to generate the final consensus […]

PMCID: 5337907
PMID: 28262711
DOI: 10.1038/srep43555

[…] neighbour-joining method with jukes-cantor and 1,000 bootstrap replicates as the nucleotide substitution model and method to test phylogeny, respectively. a circular plot was constructed using the circleator tool to demonstrate the locations of snps among the three isolates in the present study. pair-wise average nucleotide identity (ani) based on blast was calculated for the genome sequence […]

PMCID: 4988695
PMID: 27532207
DOI: 10.1371/journal.pone.0161032

[…] shown (). when contigs of strain m213 were re-ordered relative to the complete genome sequence of r. opacus b4 or r. jostii rha1, a better assembly was obtained with the latter, (). in addition, the circleator feature embedded in clovr-microbe was used to generate a graphical representation of the m213 genome (), which revealed an abundant set of unique genes and unique single nucleotide […]

PMCID: 4806288
PMID: 27010592
DOI: 10.1038/srep23635

[…] generating a multiple sequence alignment with muscle and a neighbour-joining tree using mega6 package at default settings. reads were mapped onto the genome using bwa and genome was visualized using circleator., the presence of genomic psti in g. hansenii atcc 53582, k. rhaeticus igem, g. hansenii atcc 23769 and g. xylinus e25 was searched using psti reference sequence from clostridium […]


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Circleator institution(s)
Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA; i3 Institute, University of Technology, Sydney, Australia; Department of Microbial Pathogenesis, University of Maryland Dental School, Baltimore, MD, USA; Center for Health-Related Informatics and Bioimaging, University of Maryland, College Park, MD, USA; Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, USA
Circleator funding source(s)
Supported by the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services under contract number HHSN272200900009C and grant U19AI110820.

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