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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 | # Canu
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
## Install:
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
cd canu/src
make -j <number of threads>
## Learn:
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.
## Run:
Brief command line help:
../<architecture>/bin/canu
Full list of parameters:
../<architecture>/bin/canu -options
## Citation:
- 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).
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