\textbf{Data analysis steps.}
  		(1) Autodetect analyzes TIFF images of molecules and (2) outputs BNX text files. (3) Sequence scaffolds are digested \textit{in silico} with fa2cmap\_multi producing (4) \textit{in silico} maps. (5) AssembleIryscluster uses \textit{in silico} maps, BNX files and estimated genome size to (6) normalize molecule stretch and set assembly parameters. (7) Assembler produces (8) a consensus genome map. (9) RefAligner aligns the consensus genome maps to the \textit{in silico} maps producing (10) an XMAP alignment file. (11) XMAP, of \textit{in silico} maps and consensus genome maps (see arrows with dashed lines) are used by stitch to produce (12) super scaffolded (stitched) sequence scaffolds. (13) Until no more super scaffolds are created the stitched sequence scaffolds are digested \textit{in silico} with fa2cmap\_multi producing (14) a CMAP that is aligned to (9) the consensus genome maps and steps 10-15 are iterated. Arrows with dotted rather than dashed lines are used to as input during iterations.