We have developed OnTarget, a pipeline which is designed to evaluate next generation sequencing data after sub-genomic enrichment. It is able to process single-end and paired-end sequence reads as well as single-end bisulfite data. Sequence reads can be sorted by barcodes and are mapped against the genome. Only reads which map once are processed, subsequently removing duplicate reads and finally mapping the unique reads against specified target regions in the genome. Results include statistical data as well as a graphical representation of the target coverage.