Canu

Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION). The software is currently alpha level, feel free to use and report issues encountered.

Build

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

For a quick user-quide, run:

../<achitechture>/bin/canu

For full list of options, run:

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

Docs

Canu is a hierachical 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

Read the documentation

Citation

• Berlin K, Koren S, Chin CS, Drake PJ, Landolin JM, Phillippy AM Assembling Large Genomes with Single-Molecule Sequencing and Locality Sensitive Hashing. Nature Biotechnology. (2015).
• Stay tuned for a Canu-specific citation