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Canu specifications


Unique identifier OMICS_14592
Name Canu
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input format FASTA/FASTQ
Biological technology Pacific Biosciences, Oxford Nanopore
Operating system Unix/Linux
Programming languages C, C++, Perl, Shell (Bash)
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.7
Stability Stable
Source code URL
Maintained Yes


  • TrioCanu




No version available



  • person_outline Adam Phillippy
  • person_outline Tim Phillippy

Additional information

Publications for Canu

Canu citations


High Quality Whole Genome Sequences for 77 Shiga Toxin Producing Escherichia coli Strains Generated with PacBio Sequencing

Genome Announc
PMCID: 5946054
PMID: 29748405
DOI: 10.1128/genomeA.00391-18

[…] bound to proprietary P6 version 2 polymerase and sequenced on a PacBio RS II platform using C4 chemistry for 360-min movies. The sequence reads were then filtered and assembled de novo using Falcon, Canu, or the PacBio Hierarchical Genome Assembly Process version 3 (). For 30 strains, whole-genome optical maps were generated using the Argus platform (OpGen, Gaithersburg, MD), and the sequence ord […]


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

[…] acillus phage EZ-2018a. These findings 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 […]


Complete Sequence of the Intronless Mitochondrial Genome of the Saccharomyces cerevisiae Strain CW252

Genome Announc
PMCID: 5920167
PMID: 29700138
DOI: 10.1128/genomeA.00219-18
call_split See protocol

[…] f a single run on a MinION R9.4 flow cell, using Metrichor, produced 29,276 reads with a mean length of 4 kb and a total length of 120,259 kb. The correction, trimming, and assembly of these reads by Canu version 1.4 () produced 2 contigs, one of 84 kb corresponding to the mitochondrial genome, and another of 34 kb corresponding to contamination from the nuclear genome. The mitochondrial contig wa […]


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

[…] kit P6v2 (Pacific Biosciences), loaded on two SMRTcells (Pacific Biosciences), and sequenced with 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. […]


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

[…] s (20 kb) were constructed and sequenced using 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 polishi […]


Chinook salmon (Oncorhynchus tshawytscha) genome and transcriptome

PLoS One
PMCID: 5886536
PMID: 29621340
DOI: 10.1371/journal.pone.0195461

[…] 0, -noSplitSubreads. All parameters for PBJelly were the default settings. The improved assembly, produced by PBJelly, was then used by another program that also incorporates PacBio sequences. First, Canu [] version 1.4 was used to correct the PacBio reads with a minimum length set to 2000 bp (minReadLength = 2000). The corrected PacBio reads and the improved assembly were then used by the SSPACE […]


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Canu institution(s)
Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA; Institute of Medical Microbiology, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany; Cell Wall Biology and Utilization Laboratory, ARS USDA, Madison, WI, USA; Pacific Biosciences, Menlo Park, CA, USA; Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, SA, Australia; Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia; US Meat Animal Research Center, ARS USDA, Clay Center, NE, USA
Canu funding source(s)
Supported by the Intramural Research Program of the National Human Genome Research Institute, National Institutes of Health; the University of Adelaide; the USDA-ARS Project 3040-31000-100-00D; the USDAARS Project 5090-31000-026-00-D; a grant of the Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea (grant number: HI17C2098).

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