HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads

Complete and accurate genome assemblies form the basis of most downstream genomic analyses and are of critical importance. Recent genome assembly projects have relied on a combination of noisy long-read sequencing and accurate short-read sequencing, with the former offering greater assembly continuity and the latter providing higher consensus accuracy. The recently introduced Pacific Biosciences (PacBio) HiFi sequencing technology bridges this divide by delivering long reads (>10 kbp) with high per-base accuracy (>99.9%). Here we present HiCanu, a modification of the Canu assembler designed to leverage the full potential of HiFi reads via homopolymer compression, overlap-based error correction, and aggressive…

• HH
  Howard Hughes Medical Institute
• NI
  National Institutes of Health

  Awards: HG002385, HG010169, 1F32GM134558
• NH
  National Human Genome Research Institute

  Awards: HG010169, 1R21HG010548-01, R21 1R21HG010548-01, U01 1U01HG010971, 1U01HG010971
• NI
  National Institute of General Medical Sciences

  Award: 1F32GM134558