Whole Genome Amplification (WGA) errors in the PfKE07 assembly. (A) Schematic error of WGA. DNA gets amplified (i), but then the polymerase strand switches and generates the reverse strand (ii). This generates a chimeric read that generates mis-assemblies. (B) These chimeric reads generate assembly errors, as seen in an ACT view. The top part of the reference genome (gray arrow) is duplicated in the WGA-amplified genome. The assembly errors generally occur at the contig end, so gaps are generated. Syntenic regions when comparing to the reference genome (BLAST similarity hits) are indicated in gray. Mis-assemblies (inverted similarity hits) are indicated in black.