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CODEX2 is a tool for detecting copy number variation (CNV) in high-throughput sequencing data. The CODEX2 algorithm is well suited for studies with and without negative control samples and is sensitive enough to detect rare population frequencies.


DNA structural variation; Genetic variation; Population genetics; Oncology


  • Operation: Visualisation; Genetic variation analysis; Copy number estimation
  • Software interface: Command-line user interface; Library
  • Language: R
  • Operating system: Microsoft Windows, Mac OS X, Linux
  • License: GNU GPL v2
  • Cost: Free
  • Version name: 1.3.0
  • Maturity: Stable
  • Credit: -
  • Contact: Yuchao Jiang yuchaoj _at_
  • Collection: -


Jiang Y, Wang R, Urrutia E, Anastopoulos IN, Nathanson KL, Zhang NR "CODEX2: full-spectrum copy number variation detection by high-throughput DNA sequencing." Genome Biol. 2018 Nov 26;19(1):202.
PMID: 30477554
PMCID: PMC6260772

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