Grafting of cell lines and primary tumours is a crucial step in the drug 
development process between cell line studies and clinical trials. Disambiguate 
is a program for computationally separating the sequencing reads of two species 
derived from grafted samples. Disambiguate operates on DNA or RNA-seq alignments 
to the two species and separates the components at very high sensitivity and 
specificity as illustrated in artificially mixed human-mouse samples. This 
allows for maximum recovery of data from target tumours for more accurate 
variant calling and gene expression quantification. Given that no general use 
open source algorithm accessible to the bioinformatics community exists for the 
purposes of separating the two species data, the proposed Disambiguate tool 
presents a novel approach and improvement to performing sequence analysis of 
grafted samples. Both Python and C++ implementations are available and they are 
integrated into several open and closed source pipelines. Disambiguate is open 
source and is freely available at 
https://github.com/AstraZeneca-NGS/disambiguate.