CANU

CANU is a tool to assemble long reads from either PacBio or Oxford Nanopore, which have higher error rates than short reads from Illumina. The tool runs much faster than its predecessor, Celera Assembler, and implemented some new overlapping and assembly algorithms such as adaptive overlapping strategy and sparse assembly graph construction. It can also provide output in graphical fragment assembly (GFA) format. See also the add-on: HiCanu.

Topic

Sequence assembly

Detail

  • Operation: Sequence assembly; De-novo assembly

  • Software interface: Command-line user interface

  • Language: C;Java;Perl

  • License: GPLv2

  • Cost: Free

  • Version name: 2.1

  • Credit: National Human Genome Research Institute, National Institutes of Health

  • Input: FASTA; FASTQ

  • Output: FASTA

  • Contact: adam.phillippy@nih.gov

  • Collection: -

  • Maturity: Beta

Publications

  • Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation.
  • Koren S, et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. 2017; 27:722-736. doi: 10.1101/gr.215087.116
  • https://doi.org/10.1101/gr.215087.116
  • PMID: 28298431
  • PMC: PMC5411767

Download and documentation

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