For better experience, turn on JavaScript!



FALCON is a tool for de novo assembly of long PacBio reads and it is an improved version of its predecessor HGAP. Unlike HGAP, it is a diploid-aware assembler that is better suited to assemble larger genomes. Users should look into FALCON-Unzip if they wish to phase the assembly as well.


Sequence assembly


  • Operation: Sequence assembly; De novo assembly
  • Software interface: command-line user interface
  • Language: C, Python
  • Operating system: Linux
  • License: Pacific Biosciences of California
  • Cost: Free
  • Version name: -
  • Maturity: Stable
  • Credit: National Institutes of Health; National Science Foundation
  • Contact: jchin _at_
  • Collection: FALCON


Chin CS, Peluso P, Sedlazeck FJ, Nattestad M, Concepcion GT, Clum A, Dunn C, O'Malley R, Figueroa-Balderas R, Morales-Cruz A, Cramer GR, Delledonne M, Luo C, Ecker JR, Cantu D, Rank DR, Schatz MC "Phased diploid genome assembly with single-molecule real-time sequencing." Nat Methods. 2016 Dec;13(12):1050-1054. 17.
PMID: 27749838
PMCID: PMC5503144

Download and documentation

If you find errors, please report here.