Fig. 1

A schematic showing the basic workflow and ideas behind HapSolo. The rectangles on the right illustrate the basic steps, including pre-processing (blue rectangles), steps within HapSolo (red rectangles) and post-processing (green rectangle). Some of the HapSolo steps include iterations to perform hill climbing calculations, as described in the text and shown by the arrow. On the left, step 1 shows the contigs from the primary assembly, and step 2 illustrates the all-by-all alignment of contigs. Step 3 provides examples of some properties of potential alignments. The metrics—ID, Q and QR—were defined to help capture some of the variation among these conditions. Step 4 illustrates that new primary assemblies are formed by dropping putative secondary contigs