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HGAP is a tool for de novo genome assembly using PacBio reads. It implements a hierarchical assembly process that starts with using reads that are longer than the rest as seed reads to gather all other reads for constructing a highly accurate preassembled reads. After this step, the preassembled reads can be assembled using the overlap-layout-consensus approach.


Sequence assembly


  • Operation: Sequence assembly; De novo assembly
  • Software interface: Command-line user interface
  • Language: -
  • Operating system: Linux
  • License: Not stated
  • Cost: Free
  • Version name: -
  • Maturity: Stable
  • Credit: US Department of Energy Joint Genome Institute
  • Contact: jkorlach _at_
  • Collection: -


Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, Turner SW, Korlach J "Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data." Nat Methods. 2013 Jun;10(6):563-9.
PMID: 23644548

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