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:

• 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>
  

• 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