Canu

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

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. We recommend the release version for most users.

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

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

    With clang, (default 14) needs libboost from ports.
    
      gmake
    
    With gcc (9+), can use the canu-supplied libboost or libboost from ports.
    
      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 to be 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.

      make CC=gcc-11 CXX=g++-11 BOOST=libboost  #  Ports/packages supplied boost
      make CC=gcc-11 CXX=g++-11                 #  Ports/packages supplied boost
    

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

  • Linux does not need a system installed libboost.

• 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)