Canu

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

Publication

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).

Install

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

Learn

• Quick Start - no experience or data required, download and assemble Escherichia coli today!

• FAQ - Frequently asked questions

• Canu tutorial - a gentle introduction to the complexities of canu.

• Canu pipeline - what, exactly, is canu doing, anyway?

• Canu Parameter Reference - all the parameters, grouped by function.

• Canu Command Reference - all the commands that canu runs for you.

• Canu History - the history of the Canu project.