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 quick start will get you assembling quickly, while the tutorial explains things in more detail.
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>
Brief command line help:
../<achitechture>/bin/canu
Full list of parameters:
../<architecture>/bin/canu -options
- Berlin K, Koren S, Chin CS, Drake PJ, Landolin JM, Phillippy AM Assembling Large Genomes with Single-Molecule Sequencing and Locality Sensitive Hashing. Nature Biotechnology. (2015).
- Stay tuned for a Canu-specific citation