Outline of the YGS (Y chromosome Genome Scan) method. Y-linked sequences can be efficiently identified by a comparison of the assembled genome with inexpensive short-reads obtained from female DNA: The Y-linked sequences should get no match, whereas autosomal and X-linked sequences should be nearly completely matched. Efficient removal of all types of repetitive sequences is critical because they are shared between the Y chromosome and the female DNA, and was accomplished by a straight comparison of the short DNA words (k-mers) present in the assembled genome and female short-reads. We successfully applied the YGS method to two very different genomes, D. virilis and human.