Circlator protocols

View Circlator computational protocol

Circlator specifications

Information


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
Requirements
BWA, prodigal, SAMtools, MUMmer, SPAdes
Maintained Yes

Download


Versioning


Add your version

Maintainer


  • person_outline Simon R. Harris <>

Publication for Circlator

Circlator in pipelines

 (2)
2018
PMCID: 5762679
PMID: 29321680
DOI: 10.1038/s41598-017-18910-w

[…] oxford, uk), which generated 477.161 reads (30.9 gb) and was converted into a single fastq file of 2 gb using poretools. the assembly of reads were performed using canu with default settings. circlator was then used to locate and circularize complete chromosome and plasmids in the draft assembly. contigs representing the chromosome and plasmids were subsequently polished using nanopolish […]

2017
PMCID: 5609411
PMID: 28935732
DOI: 10.1128/genomeA.00939-17

[…] option. the resulting single scaffold was improved using pilon version 1.22 software (). we circularized this gapless chromosome sequence and rearranged it to start at the dnaa gene using the circlator software (). we then assembled the genome of strain gur using an identical procedure, with the following modifications: different k-mers with “-k 33,55,77,99,121,143” and providing […]


To access a full list of citations, you will need to upgrade to our premium service.

Circlator in publications

 (60)
PMCID: 5920177
PMID: 29700165
DOI: 10.1128/genomeA.00364-18

[…] 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 […]

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

[…] 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, https://github.com/pacificbiosciences/smrt-analysis). […]

PMCID: 5897814
PMID: 29650567
DOI: 10.1128/genomeA.00176-18

[…] 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 […]

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 […]

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

[…] 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 […]


To access a full list of publications, you will need to upgrade to our premium service.

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

Circlator reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review Circlator