A single molecule sequence assembler for genomes large and small.
C++ C Perl Makefile Shell CSS Python



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 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


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>


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


Brief command line help:


Full list of parameters:

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