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

Canu is a hierachical 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

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

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

Alternatively, you can also build the latest unreleased from github:

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

Brief command line help:

../<achitechture>/bin/canu

Full list of parameters:

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

• Berlin K, Koren S, Chin CS, Drake PJ, Landolin JM, Phillippy AM Assembling Large Genomes with Single-Molecule Sequencing and Locality Sensitive Hashing. Nature Biotechnology. (2015).
• Stay tuned for a Canu-specific citation