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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: