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ACE is an R tool package for evaluating absolute copy number variation (CNV) and estimates tumor purity and ploidy. The algorithm uses low coverage whole genome sequencing (WGS) reads and obtains data segments from the QCDA pipeline, which puts the sequenced read into bins. ACE computes and fits the segment length by iteratively measuring error rates, using the root mean square error (RMSE) or mean absolute error (MAE). The Authors claim ACE to perform better than ABSOLUTE and ichorCNA algorithms.


Genetics; Structural genomics; Oncology


  • Operation: Genotyping; Variant detection; Copy number estimation
  • Software interface: Command-line user interface
  • Language: R
  • Operating system: Microsoft Windows, Mac OS X, Linux
  • License: GNU GPL v2
  • Cost: Free
  • Version name: 1.2.0
  • Credit: Supported by a Cancer Center Amsterdam institutional grant.
  • Contact: Ruud H. Brakenhoff rh.brakenhoff _at_ | Jos B. Poell j.poell _at_
  • Collection: -


Poell JB, Mendeville M, Sie D, Brink A, Brakenhoff RH, Ylstra B "ACE: absolute copy number estimation from low-coverage whole-genome sequencing data." Bioinformatics. 2019 Aug 15;35(16):2847-2849. 10.1093/bioinformatics/bty1055.
PMID: 30596895

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