Unicycler pipeline

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



Add your version



  • person_outline Ryan Wick <>

Publication for Unicycler

Unicycler IN pipelines

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 (11). the assembly was polished with unicycler_polish using all sequence reads and scaffolded with links v1.8.5 (12) using nanopore reads. assembly gaps were closed with sealer v1.5.2 using […]

PMCID: 5695209
PMID: 29177090
DOI: 10.1099/mgen.0.000132

[…] we assembled each genome using a combination of ont reads and previously available illumina reads, and little to no manual intervention was needed to achieve fully resolved assemblies using the unicycler hybrid assembler. assembling only ont reads with canu was less effective, resulting in fewer resolved genomes and higher error rates even following error correction with nanopolish. […]

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

Unicycler reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review Unicycler