Unicycler protocols

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Unicycler specifications

Information


Unique identifier OMICS_14591
Name Unicycler
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages C++
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Requirements
Python, SPAdes, Pilon, Java, Bowtie2, Samtools, BLAST +
Maintained Yes

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Maintainer


  • person_outline Ryan Wick <>

Publication for Unicycler

Unicycler in pipelines

 (3)
2018
PMCID: 5909648
PMID: 29579234
DOI: 10.1093/femsle/fny069

[…] quality of the nanopore reads was assessed using nanoplot., the genome was first assembled with spades, version 3.11.1 using default parameters (bankevich et al.) using ion pgm reads only, then with unicycler, version v0.4.3 (wick et al.) also using default parameters with both ion pgm and nanopore reads. for the latter, the genome was polished with racon (vaser et al.) and pilon (walker et al.). […]

2017
PMCID: 5597760
PMID: 28912319
DOI: 10.1128/genomeA.00963-17

[…] preparation protocol and miseq reagent kit v3 (illumina, san diego, ca, usa)., nanopore sequence reads were filtered using nanopolish v0.5.0 and assembled de novo concurrently with miseq reads using unicycler (). the assembly was polished with unicycler_polish using all sequence reads and scaffolded with links v1.8.5 () using nanopore reads. assembly gaps were closed with sealer v1.5.2 using […]

2017
PMCID: 5701470
PMID: 29167245
DOI: 10.1128/genomeA.01298-17

[…] and sequenced using the illumina hiseq 2500 paired-end 125-bp platform. in addition, the oxford nanopore minion sequencing platform (2d sequencing) was used to generate long sequence reads (). the unicycler version 0.4.0 () and spades version 3.10.1 () pipelines were used to assemble the genome. a hybrid alignment strategy was employed to assemble the genome using long reads generated […]


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Unicycler in publications

 (22)
PMCID: 5897807
PMID: 29650575
DOI: 10.1128/genomeA.00258-18

[…] trimming and filtering of illumina reads were performed using the bbtools software suite (http://jgi.doe.gov/data-and-tools/bbtools/). hybrid assembly of illumina and pacbio reads was performed with unicycler v0.4.4 (), a wrapper tool using minimap v2.5-r622-dirty (), racon v0.5.0 (), spades v3.11.1 (), and pilon v1.22 (). annotation of the final assemblies was done by the national center […]

PMCID: 5887029
PMID: 29622618
DOI: 10.1128/genomeA.00237-18

[…] shotgun paired-end sequencing libraries, which were sequenced with a miseq instrument and the miseq reagent kit version 3 as recommended by the manufacturer (illumina, san diego, ca, usa). the unicycler pipeline () was used for the combined assembly of the nanopore and the illumina reads. the assembly resulted in one circular replicon with a size of 1,714,918 bp and an overall g+c content […]

PMCID: 5887031
PMID: 29622605
DOI: 10.1128/genomeA.00036-18

[…] ca), generating 2 × 250-bp reads, and the minion instrument (oxford nanopore, oxford, uk) in order to close the first genomes of this lineage. the illumina and minion reads were assembled using unicycler v0.4.1 (). genome annotation was performed at the genbank submission step using the prokaryotic genome automatic annotation pipeline (pgaap) from ncbi ()., the genome of the st25 s. […]

PMCID: 5909648
PMID: 29579234
DOI: 10.1093/femsle/fny069

[…] quality of the nanopore reads was assessed using nanoplot., the genome was first assembled with spades, version 3.11.1 using default parameters (bankevich et al.) using ion pgm reads only, then with unicycler, version v0.4.3 (wick et al.) also using default parameters with both ion pgm and nanopore reads. for the latter, the genome was polished with racon (vaser et al.) and pilon (walker et al.). […]

PMCID: 5864954
PMID: 29567740
DOI: 10.1128/genomeA.00175-18

[…] ∼496×). illumina paired-end sequencing generated 1.2 million 2 × 250-bp reads (coverage, ∼182×). hybrid assembly of the genome using both short (illumina) and long (pacbio) reads was done using the unicycler pipeline ()., the genome assembly produced two large scaffolds of 2,121,368 and 1,177,802 bp in length, representing the two b. melitensis chromosomes. the sizes of the chromosomes […]


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Unicycler institution(s)
Centre for Systems Genomics, The University of Melbourne, Victoria, Australia; Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, Australia

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