Canu

Canu is a fork of the Celera Assembler, designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION).

Canu is a hierarchical assembly pipeline which runs in four steps:

Install:

Do NOT download the .zip source code. It is missing files and will not compile. This is a known flaw with git itself.
The easiest way to get started is to download a binary release.
Installing with a 'package manager' is not encouraged, but if you have no other choice:
- Conda: conda install -c conda-forge -c bioconda -c defaults canu
- Homebrew: brew install brewsci/bio/canu
Alternatively, you can use the latest unreleased version from the source code. This version 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.
```
  git clone https://github.com/marbl/canu.git
  cd canu/src
  make -j <number of threads>
```
An unsupported Docker image made by Frank Förster is at https://hub.docker.com/r/greatfireball/canu/.

The quick start will get you assembling quickly, while the tutorial explains things in more detail.

Brief command line help:

../<architecture>/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. Genome Research. (2017). doi:10.1101/gr.215087.116
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)