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Circlator specifications


Unique identifier OMICS_09488
Name Circlator
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
BWA, prodigal, SAMtools, MUMmer, SPAdes
Maintained Yes




No version available


  • person_outline Simon R. Harris

Publication for Circlator

Circlator citations


Complete Genome Sequences of Two Bacillus pumilus Strains from Cuatrociénegas, Coahuila, Mexico

Genome Announc
PMCID: 5920177
PMID: 29700165
DOI: 10.1128/genomeA.00364-18
call_split See protocol

[…] s will give insights into understanding the establishment of biological interactions. Total genomic DNA was sequenced with the PacBio RS II system, assembled with Canu v.1.3 (), and circularized with Circlator v.1.3 (). The B. pumilus 145 assembly resulted in two contigs representing the chromosome (3,937,399 bp, 265.81× mean coverage) and the Bacillus phage EZ-2018a (118,485 bp, 486.825× mean cov […]


Horizontal antimicrobial resistance transfer drives epidemics of multiple Shigella species

Nat Commun
PMCID: 5899146
PMID: 29654279
DOI: 10.1038/s41467-018-03949-8

[…] as extracted using the MasterPure Complete DNA and RNA extraction kit and sequenced on the Pacific Biosciences Sequel, and the data was assembled as follows: assembly by HGAPv3; circularisation using Circlator v1.1.3; and polishing by Quiver v1 (SMRT-analysis: a software suite for analysing single-molecule, real-time DNA sequencing data, SMRT-s […]


Genome Sequence of a Multidrug Resistant Candida haemulonii Isolate from a Patient with Chronic Leg Ulcers in Israel

Genome Announc
PMCID: 5897814
PMID: 29650567
DOI: 10.1128/genomeA.00176-18
call_split See protocol

[…] th C4-V2 chemistry (Pacific Biosciences) for 360-min movies.Sequence reads were de novo assembled using Canu version 1.6 (). The resultant contigs were checked for further joins and circularity using Circlator version 1.5 (). Contigs were polished using Quiver, part of the SMRT Analysis suite version 2.3 (Pacific Biosciences) (), and the sequence order was verified using the restriction enzyme Afl […]


Genomic analysis of oral Campylobacter concisus strains identified a potential bacterial molecular marker associated with active Crohn’s disease

PMCID: 5893538
PMID: 29636463
DOI: 10.1038/s41426-018-0065-6

[…] the PacBio RS II platform (Ramaciotti Centre for Genomics, University of New South Wales, Australia). The PacBio reads were assembled into contigs using CANU v 1.3. The assembly was rearranged using Circlator to produce accurate linear representations of circular sequences. The assembly was then subjected to polishing using Quiver, followed by polishing with Illumina reads obtained from our previ […]


Genome Sequence of the Amphotericin B Resistant Candida duobushaemulonii Strain B09383

Genome Announc
PMCID: 5876483
PMID: 29599161
DOI: 10.1128/genomeA.00204-18

[…] d with C4 v2 chemistry (Pacific Biosciences) for 360-minute movies.Sequence reads were de novo assembled using Canu v1.6 (). The resultant contigs were checked for further joins and circularity using Circlator v1.5 (). Contigs were polished using Quiver, part of SMRT analysis suite v2.3 (Pacific Biosciences) (), and the sequence order was verified using restriction enzyme AflII whole-genome mappin […]


A new strategy to infer circularity applied to four new complete frog mitogenomes

Ecol Evol
PMCID: 5916287
PMID: 29721275
DOI: 10.1002/ece3.3918

[…] yers, & Lipman, ) and comparing the size of the assembled genome to the reference (Soorni, Haak, Zaitlin, & Bombarely, ). Additionally, tools such as Minimus2 (Sommer, Delcher, Salzberg, & Pop, ) and Circlator (Hunt et al., ) perform circularization of genome assemblies by joining individual contigs, although they do not clip circular fragments included in larger scaffolds and focus only on identi […]


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Circlator institution(s)
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK

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