Fig. 1

X-shredding target site selection. a Overview of the kmer selection pipeline and steps involved in the final selection. b Plot showing coverage in Illumina (sum) and PacBio (Hits_Sum) datasets of all redkmer output candidate X-kmers. The top 25 selected and targetable kmers resulting from the manual downstream selection are shown in pink, and those experimentally validated are shown along with their sequence. c Explanatory representation of the selection criteria used (abundance, frequency and occurrence) and how they relate to Illumina (male, blue; female, pink) and PacBio (male only) datasets shown here for an example kmer (grey). Illumina reads are represented in the top row with short rectangles colour-coded according to sex-specific (male in blue and female in pink) libraries. PacBio reads are represented in the bottom row with longer rectangles, only in blue because the PacBio library is derived from male-only genomic DNA. The example kmer is shown in grey dots, and its occurrence in the two types of sequencing datasets is shown in d in green numbers in parentheses. For example, coverage in Illumina datasets is 5 because the kmer occurs 5 times in the male and female Illumina libraries, and coverage in PacBio is 8 because the kmer occurs 5 times in the PacBio reads. d Distribution of the redkmer-selected candidate X-kmers for the selection criteria (x-axis and plot labels—see the “Methods” section) including the top 25 (in pink) and tested kmers. The plots show the kmer abundance in the Illumina (sum) and PacBio (hits_sum) and the maximum occurrence in a single PacBio read (max.pt—frequency) and the total number of unique PacBio reads that contain it (Unique_bin_Occurence). The green number in parenthesis next to the criterion label (top) shows the respective value of the example kmer shown in c and its interaction with the example Illumina and PacBio libraries