For better experience, turn on JavaScript!



Magnolya is a tool to detect copy number variation (CNV) within two individual genome sequences. The Magnolya algorithm uses a Poisson mixture model to identify CNV between two genomes by joining the strings into a single assembly, creates a graph, and traverses the edges and nodes to infer the CNV probabilities. This approach eliminates the need for segmentation of the genomic regions and mapping to a reference genome.


Whole genome sequencing; Genetics; Genetic variation


  • Operation: Copy number estimation
  • Software interface: Command-line user interface
  • Language: Python
  • Operating system: Linux
  • License: Not stated
  • Cost: Free
  • Version name: 0.15
  • Credit: The Kluyver Centre for Genomics of Industrial Fermentation, supported by the Netherlands Genomics Initiative.
  • Contact: Saskia Peters S.Peters _at_ | Thomas Abeel T.Abeel _at_
  • Collection: -


Nijkamp JF, van den Broek MA, Geertman JM, Reinders MJ, Daran JM, de Ridder D "De novo detection of copy number variation by co-assembly." Bioinformatics. 2012 Dec 15;28(24):3195-202. Epub 2012 Oct 9.
PMID: 23047563

Download and documentation

If you find errors, please report here.