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 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>
The quick start will get you assembling quickly, while the tutorial explains things in more detail.
Brief command line help:
../<achitechture>/bin/canu
Full list of parameters:
../<architecture>/bin/canu -options
- 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).