A single molecule sequence assembler for genomes large and small.
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README.md

Canu

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

Install:

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>

Learn:

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

Run:

Brief command line help:

../<achitechture>/bin/canu

Full list of parameters:

../<architecture>/bin/canu -options

Citation: