\textbf{Assembly workflow for assemble\_SGE\_cluster.pl.}
  		(A) The Irys instrument produces tiff files that are converted into BNX text files. (B) One BNX file is produced for each flowcell on a IrysChip. (C) BNX files are split by scan and aligned to the sequence reference. Stretch (bases per pixel) is recalculated for each scan from the alignment. (D) Quality check graphs are created for each pre-adjusted flowcell BNX. (E) Adjusted flowcell BNXs are merged. (F) The first assemblies are run with a variety of p-value thresholds. (G) The best first assembly (red oval) is chosen and a version of this assembly is produced with a variety of minimum molecule length filters.