Canu is a fork of the Celera Assembler, designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION).

Canu is a hierarchical assembly pipeline which runs in four steps:

• Detect overlaps in high-noise sequences using MHAP
• Generate corrected sequence consensus
• Trim corrected sequences
• Assemble trimmed corrected sequences

Caution

Canu has reached END OF LIFE. It hasn't seen active development since around 2021 and has not been tuned or tested on more recent data. Unless you're assembling reads from that era, use a more recent assembler, such as Flye, Hifiasm or Verkko.

Dark and Stormy until HiCanu sees the Light, the Genome Research cover image by Arang Rhie.

Install:

• Do NOT download the .zip source code. It is missing files and will not compile. This is a known flaw with git itself.

• The easiest way to get started is to download a binary release.

• Installing with a 'package manager' is not encouraged, but if you have no other choice:

  • Conda: conda install -c conda-forge -c bioconda -c defaults canu
  • Homebrew: brew install brewsci/bio/canu

• Alternatively, you can use the latest unreleased version from the source code. This version has not undergone the same testing as a release and so may have unknown bugs or issues generating sub-optimal assemblies. Depending on your operating system (see below), additional packages will need to be installed.

    git clone https://github.com/marbl/canu.git
    cd canu/src
    make -j <number of threads>
  

  • Linux needs some development packages installed. Installing libboost1.83-all-dev is perhaps advised, as it is more recent than the one included in Canu, but not required.

    On Ubuntu:
    
      apt install zlib1g-dev libcurl4-openssl-dev libssl-dev liblzma-dev libbz2-dev
    

  • FreeBSD generally requires libboost installed from packages/ports. It will compile with either clang (>= 14) or gcc (>= 9). It requires openjdk18.

    With clang, libboost MUST be installed from ports.
    
      gmake
    
    With gcc, either the canu-supplied or ports-supplied libboost can be used.
    
      gmake CC=gcc9 CXX=g++9 BOOST=libboost    #  Canu-supplied boost
      gmake CC=gcc9 CXX=g++9                   #  Ports/packages supplied boost
    

  • MacOS Apple Silicon requires libboost, and either openjdk or oracle-jdk installed from homebrew (preferred) or MacPorts. It will compile with either clang (>=14) or gcc (>= 9) but WILL NOT compile with the standard Xcode compiler.

      brew install llvm openjdk boost
      make CC=gcc-11 CXX=g++-11 BOOST=libboost  #  Canu-supplied boost
      make CC=gcc-11 CXX=g++-11                 #  Ports/packages supplied boost
    
    You might need to add the following to .zshrc:
    
      export JAVA_HOME=/opt/homebrew/opt/openjdk
    

  • MacOS Intel is probably the same as Apple Silicon, but not tested.

• An unsupported Docker image made by Frank Förster is at https://hub.docker.com/r/greatfireball/canu/.

Learn:

The quick start will get you assembling quickly, while the tutorial explains things in more detail.

Run:

Brief command line help:

../<architecture>/bin/canu

Full list of parameters:

../<architecture>/bin/canu -options

Citation:

• Koren S, Walenz BP, Berlin K, Miller JR, Phillippy AM. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Research. (2017). doi:10.1101/gr.215087.116
• Koren S, Rhie A, Walenz BP, Dilthey AT, Bickhart DM, Kingan SB, Hiendleder S, Williams JL, Smith TPL, Phillippy AM. De novo assembly of haplotype-resolved genomes with trio binning. Nature Biotechnology. (2018). (If you use trio-binning)
• Nurk S, Walenz BP, Rhiea 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. biorXiv. (2020). (If you use -pacbio-hifi)