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Sequenza package provides tools to genotyping cancer samples, cancer cellularity, ploidy, copy number variation (CNV), and infer alleles that are mutated.


Genetics; DNA structural variation; Oncology


  • Operation: Polymorphism detection; Sequence analysis; Structural variation detection
  • Software interface: Command-line user interface; Library
  • Language: R:Python
  • Operating system: Microsoft Windows, Mac OS X, Linux
  • License: GNU General Public License v3
  • Cost: Free
  • Version name: 3.0.0
  • Maturity: Stable
  • Credit: The European Commission 7th Framework Programme, the Danish Council for Independent Research.
  • Contact: favero.francesco at
  • Collection: -


Favero F, Joshi T, Marquard AM, Birkbak NJ, Krzystanek M, Li Q, Szallasi Z, Eklund AC "Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data." Ann Oncol. 2015 Jan;26(1):64-70.
PMID: 25319062
PMCID: PMC4269342

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