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Figure 1 The principle and some applications of Strand-seq. (A) Strand-seq involves sequencing template strands. Parental homologues (pink and blue) are double stranded; Crick (C) strand in blue, Watson (W) strand in orange. DNA replication occurs in the presence of BrdU, which incorporates into the replicated strand (dotted lines). Sequencing libraries from single daughter cells have BrdU-containing strand selectively removed to generate directional chromosomes; either CC, WW (top) or WC (bottom) depending on segregation. Histograms of directional reads are plotted on ideograms for each chromosome. (B) When homologues inherit different template strands, haplotypes can be determined. In the example, all C reads map to the maternal homologue so all single nucleotide variants (SNVs) identified (black dots) form the maternal haplotype, and all W reads map to the paternal homologue, so all SNVs identified (white dots) form the paternal haplotype. (C) Structural variation can be identified in Strand-seq libraries. Inversions will align to the opposite strand of the reference assembly and as so be identified as a change in template strand state (D) Strand-seq can be used to create assemblies since contigs from the same chromosome will have the same template inheritance pattern. Grouping based on shared template inheritance patterns determines which fragments belong together. Note in the example contigs from ch1, chr3, and chr5 have the same template pattern (WC) so require additional libraries to establish which contigs belong to which chromosome.