Fig. 9

Alignments of long-reads and short-reads against one inferred haplotype: This screenshot from IGV (Integrative Genomics Viewer) shows PacBio reads (upper panel) and Illumina reads (lower panel) aligned to one of the inferred haplotype sequences prior to manual correction. The alignments are easily visualised using configuration files automatically generated by DR2S. This example demonstrates remaining ambiguities in the short-reads at positions 790 and 809. These positions were also observed in the final mapping plot. The long-reads at these positions are unambiguous and can be used to guide the manual edit