Fig. 5

Overview of DiscoverY. A male genome is sequenced and assembled into contigs, which are colored red (autosomes), green (X chromosome), and blue (Y chromosome). In parallel, a female reference is k-merized and proportion shared with female is computed for each contig (female proportion). Additionally, the median k-mer abundance for each contig is calculated based on the male raw reads used for assembly (male depth of coverage). The vertical line (short dashes) indicates a threshold chosen in female_only mode, using only the female proportion. In this mode, those contigs with low proportion shared with female reference are classified as Y-chromosomal. The diagonal line (long dashes) indicates a threshold chosen in best mode, using both female proportion and male coverage. In this mode, those contigs with low-to-moderate proportion shared with female reference and low depth of coverage from male read k-mers are classified as Y- chromosomal. The pair of dotted lines indicates a threshold chosen in female+male mode. In this mode, the user can manually try different combinations of female proportion and male coverage to retrieve Y chromosomal contigs