Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION).
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).
Koren S, Rhie A, Walenz BP, Dilthey AT, Bickhart DM, Kingan SB, Hiendleder S, Williams JL, Smith TPL, Phillippy AM. De novo assembly of haplotype-resolved genomes with trio binning. Nature Biotechnology. (2018). (If you use trio-binning)
Nurk S, Walenz BP, Rhiea A, Vollger MR, Logsdon GA, Grothe R, Miga KH, Eichler EE, Phillippy AM, Koren S. HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads. biorXiv. (2020). (If you use -pacbio-hifi)
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>
- 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.