Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separation

Long-read single-molecule sequencing has revolutionized de novo genome assembly and enabled the automated reconstruction of reference-quality genomes. However, given the relatively high error rates of such technologies, efficient and accurate assembly of large repeats and closely related haplotypes remains challenging. We address these issues with Canu, a successor of Celera Assembler that is specifically designed for noisy single-molecule sequences. Canu introduces support for nanopore sequencing, halves depth-of-coverage requirements, and improves assembly continuity while simultaneously reducing runtime by an order of magnitude on large genomes versus Celera Assembler 8.2. These advances result from new…

• NS
  National Science Foundation

  Awards: NSF IOS-1237993, IOS-1237993, 1237993
• UD
  U.S. Department of Homeland Security

  Award: HSHQDC-07-C-00020
• B
  Battelle
• NI
  National Institutes of Health

  Award: HSHQDC-07-C-00020
• SA
  Science and Technology Directorate

  Award: HSHQDC-07-C-00020
• NH
  National Human Genome Research Institute
• DO
  Division of Integrative Organismal Systems