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Unicycler specifications


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
Python, SPAdes, Pilon, Java, Bowtie2, Samtools, BLAST +
Maintained Yes




No version available



  • person_outline Ryan Wick

Publication for Unicycler

Unicycler citations


Genome Sequences of Five Mycobacterium bovis Strains Isolated from Farmed Animals and Wildlife in Canada

Genome Announc
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 for Bio […]


Complete Genome Sequence of the Methanococcus maripaludis Type Strain JJ (DSM 2067), a Model for Selenoprotein Synthesis in Archaea

Genome Announc
PMCID: 5887029
PMID: 29622618
DOI: 10.1128/genomeA.00237-18
call_split See protocol

[…] lumina 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 o […]


The Genome Sequence of “Candidatus Fokinia solitaria”: Insights on Reductive Evolution in Rickettsiales

Genome Biol Evol
PMCID: 5905368
PMID: 29659807
DOI: 10.1093/gbe/evy072

[…] DNA was subjected to Pacific Biosciences Sequel sequencing, obtaining 12,243,617 reads. All PacBio reads and the selected Illumina reads were used to perform a second assembly step using the software Unicycler (). The softwares Bandage () and BLAST were then used to manually perform bioinformatic joins on the result of this second assembly. The obtained genome was annotated using Prokka () followe […]


Community led comparative genomic and phenotypic analysis of the aquaculture pathogen Pseudomonas baetica a390T sequenced by Ion semiconductor and Nanopore technologies

FEMS Microbiol Lett
PMCID: 5909648
PMID: 29579234
DOI: 10.1093/femsle/fny069
call_split See protocol

[…] nd 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.). […]


PlasmidTron: assembling the cause of phenotypes and genotypes from NGS data

Microb Genom
PMCID: 5885016
PMID: 29533742
DOI: 10.1099/mgen.0.000164

[…] ltering the dataset, a higher qualityassembly is possible. However, if the copy number of the plasmids is similar to that of the chromosome, it is difficult to separate out candidate plasmid contigs. Unicycler [] is a hybrid assembler that can combine short- and long-read data to produce fully circularized chromosomes and plasmids. It essentially fixes many of the deficiencies of SPAdes[] and fine […]


Emergence of an Extensively Drug Resistant Salmonella enterica Serovar Typhi Clone Harboring a Promiscuous Plasmid Encoding Resistance to Fluoroquinolones and Third Generation Cephalosporins

PMCID: 5821095
PMID: 29463654
DOI: 10.1128/mBio.00105-18

[…] A hybrid assembly was performed using both the short- and long-read sequencing data for BL60006 using Unicycler (v0.4.0) (). A single circularized chromosome and a single plasmid were assembled. As a region was shared between the plasmid and chromosome, further sequencing using the PacBio RSII was req […]


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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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