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CANU is a tool to assemble long reads from either PacBio or Oxford Nanopore, which have higher error rates than short reads from Illumina. The tool runs much faster than its predecessor, Celera Assembler, and implemented some new overlapping and assembly algorithms such as adaptive overlapping strategy and sparse assembly graph construction. It can also provide output in graphical fragment assembly (GFA) format. See also the add-on: HiCanu.


Sequence assembly


  • Operation: Sequence assembly; De-novo assembly
  • Input: FASTA; FASTQ
  • Output: FASTA
  • Software interface: Command-line user interface
  • Language: C;Java;Perl
  • Operating system: Linux; Mac OS X
  • License: GPLv2
  • Cost: Free
  • Version name: 2.1
  • Maturity: Beta
  • Credit: National Human Genome Research Institute, National Institutes of Health
  • Contact: adam.phillippy _at_
  • Collection: -


Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM "Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation." Genome Res. 2017 May;27(5):722-736. Epub 2017 Mar 15.
PMID: 28298431
PMCID: PMC5411767

Download and documentation

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