Contamination detection in mtDNA

Haplocheck detects in-sample contamination in mtDNA or WGS sequencing studies by analyzing the mitchondrial content.

The main features of haplocheck are:


Hansi Weissensteiner,
Senior Scientist

+43 512 9003 70564
Sebastian Schönherr, Dr.techn.
Professor of Digital and Computational Genomics

+43 512 9003 70579
Lukas Forer, PhD
Assistant Professor of Genome Informatics

+43 512 9003 70562


Haplocheck is available as a graphical web-service or on GitHub for local usage.


Full documentation for haplocheck can be found here.


Weissensteiner H, Forer L, Fendt L, Kheirkhah A, Salas A, Kronenberg F, Schoenherr S: Contamination detection in sequencing studies using the mitochondrial phylogeny. Genome Res. 31:309-316, 2021. PMID: 33452015   Journal Article