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


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. bioRxiv. (2016).


The easiest way to get started is to download a release. If you encounter any issues, please report them using the github issues page.

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

git clone
cd canu/src
make -j <number of threads>