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HiCANU is an add-on assembly tool to the popular long read Canu assembler. The assembler is still called Canu but has the added option to read PacBio HiFi reads using ‘-pacbio-hifi’. The main advantage of this tool is the ability to use the highly accurate and long HiFi reads for genome assembly. The algorithm implements homopolymer compression, overlap-based error correction, and aggressive false overlap filtering.


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
  • Credit: National Human Genome Research Institute, National Institutes of Health
  • Contact: sergey.koren _at_
  • Collection: -


Nurk S, Walenz BP, Rhie A, Vollger MR, Logsdon GA, Grothe R, Miga KH, Eichler EE, Phillippy AM, Koren S "HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads." Genome Res, 2020
PMID: 32801147

Download and documentation

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