Canu is a fork of the [Celera Assembler](http://wgs-assembler.sourceforge.net/wiki/index.php?title=Main_Page), designed for high-noise single-molecule sequencing (such as the [PacBio](http://www.pacb.com) [RS II](http://www.pacb.com/products-and-services/pacbio-systems/rsii/)/[Sequel](http://www.pacb.com/products-and-services/pacbio-systems/sequel/) or [Oxford Nanopore](https://www.nanoporetech.com/) [MinION](https://nanoporetech.com/products)).
Canu is a hierarchical assembly pipeline which runs in four steps:
* Detect overlaps in high-noise sequences using [MHAP](https://github.com/marbl/MHAP)
* Generate corrected sequence consensus
* Trim corrected sequences
* Assemble trimmed corrected sequences
The easiest way to get started is to download a [release](http://github.com/marbl/canu/releases).
Alternatively, you can also build the latest unreleased from github:
git clone https://github.com/marbl/canu.git
make -j <number of threads>
The unreleased tip 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.
The [quick start](http://canu.readthedocs.io/en/latest/quick-start.html) will get you assembling quickly, while the [tutorial](http://canu.readthedocs.io/en/latest/tutorial.html) explains things in more detail.
Brief command line help:
Full list of parameters:
- 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](https://doi.org/10.1101/gr.215087.116). Genome Research. (2017).