# Canu

**Repository Path**: mirrors/Canu

## Basic Information

- **Project Name**: Canu
- **Description**: Canu 是一个高噪声单分子测序工具，类似于 PacBio RSII 和 Oxford Nanopore MinION
- **Primary Language**: C
- **License**: GPL-2.0
- **Default Branch**: master
- **Homepage**: https://www.oschina.net/p/canu
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 2
- **Created**: 2019-12-23
- **Last Updated**: 2025-09-13

## Categories & Tags

**Categories**: mathlibs

**Tags**: None

## README

<a href="documentation/HiCanu_Genome_Research.jpg"><img src="documentation/HiCanu_Genome_Research_Small.jpg" align="right" title="Dark and Stormy until HiCanu sees the Light, the Genome Research cover by Arang Rhie."></a>

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

>[!CAUTION]
>Canu has reached END OF LIFE.  It hasn't seen
active development since around 2021 and has not been tuned or tested on
more recent data.  Unless you're assembling reads from that era,
use a more recent assembler, such as
[Flye](https://github.com/mikolmogorov/Flye),
[Hifiasm](https://github.com/chhylp123/hifiasm) or
[Verkko](https://github.com/marbl/verkko).

*Dark and Stormy until HiCanu sees the Light*, the Genome Research cover image by [Arang Rhie](https://genomeinformatics.github.io/people/rhie/).

## Install:

* Do NOT download the .zip source code.  It is missing files and will not compile.  This is a [known flaw](https://github.com/dear-github/dear-github/issues/214) with git itself.

* The easiest way to get started is to download a binary [release](http://github.com/marbl/canu/releases).

* 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.
  Depending on your operating system (see below), additional packages will
  need to be installed.

        git clone https://github.com/marbl/canu.git
        cd canu/src
        make -j <number of threads>

  * Linux needs some development packages installed.  Installing
    libboost1.83-all-dev is perhaps advised, as it is more recent than the one
    included in Canu, but not required.

        On Ubuntu:

          apt install zlib1g-dev libcurl4-openssl-dev libssl-dev liblzma-dev libbz2-dev

  * FreeBSD generally requires libboost installed from packages/ports.  It
    will compile with either clang (>= 14) or gcc (>= 9).  It requires
    openjdk18.

        With clang, libboost MUST be installed from ports.

          gmake

        With gcc, either the canu-supplied or ports-supplied libboost can be used.

          gmake CC=gcc9 CXX=g++9 BOOST=libboost    #  Canu-supplied boost
          gmake CC=gcc9 CXX=g++9                   #  Ports/packages supplied boost

  * MacOS Apple Silicon requires libboost, and either openjdk or oracle-jdk
    installed from homebrew (preferred) or MacPorts.  It will compile
    with either clang (>=14) or gcc (>= 9) but WILL NOT compile with the
    standard Xcode compiler.

          brew install llvm openjdk boost
          make CC=gcc-11 CXX=g++-11 BOOST=libboost  #  Canu-supplied boost
          make CC=gcc-11 CXX=g++-11                 #  Ports/packages supplied boost

        You might need to add the following to .zshrc:

          export JAVA_HOME=/opt/homebrew/opt/openjdk

  * MacOS Intel is probably the same as Apple Silicon, but not tested.

* An *unsupported* Docker image made by Frank Förster is at https://hub.docker.com/r/greatfireball/canu/.

## 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). `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](http://doi.org/10.1038/nbt.4277).  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](https://doi.org/10.1101/2020.03.14.992248).  biorXiv.  (2020). (If you use -pacbio-hifi)