Fig. 1

Bioinformatic workflow overview. There were three entry points of data, shown by boxes with white shading: Illumina read data, PacBio read data and OpGen optical map data. Boxes shaded in dark blue show work done by the assembly pipeline in a semi-automated fashion: quality control (and trimming) of short-read Illumina data, Illumina-only assemblers, evaluation of assembly quality (for all assemblies) using feature-response curves and standard metrics, preparing two chosen assemblies for in silico digestion and optical map placement and finally using open_util.py to generate an assembly from the scaffold-optical map placement coordinates. Work done outside the assembly pipeline is shown as boxes with light blue shading: the PacBio-only assemblies, the PacBio-Illumina hybrid assemblies and the operation of OpGen’s Mapsolver software for in silico digestion and placement of scaffolds and their placement on optical maps