Canu protocols

Canu computational protocol

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



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  • person_outline Adam Phillippy <>
  • person_outline Tim Phillippy <>

Additional information

Publications for Canu

Canu IN pipelines

PMCID: 5571409
PMID: 28839023
DOI: 10.1128/genomeA.00829-17

[…] bluepippin (sage science, beverly, ma) and sequenced using pacbio’s p6-c4 chemistry using 240-min movies. the total raw data generated was 47×. reads were trimmed, corrected, and assembled using the canu assembler version 1.2 (6). the final assembled genome consisted of 451 mbp in 4,577 contigs, with 12.7× mean coverage. the largest contig size was 3,055,912 bp. scaffolds (2,396) were generated […]

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

[…] 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. we demonstrate that multiplexed ont sequencing is a valuable tool […]

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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