Figure 6. PLACNET flow diagram.

The diagram represents the PLACNET workflow to analyze an Illumina bacterial genome dataset. It can be separated in two sub-process: network delineation and plasmid analysis. Network delineation consists on contig assembly, determination of scaffold interactions, reference search of homologous genomes and plasmid protein prediction. Plasmid analysis basically consists in the construction of a dendrogram of plasmid protein profiles, which identifies the most relevant reference sequences, followed by plasmid cluster analysis, which compares query plasmids with its closest references. Plasmid analysis is a feedback process that helps to resolve uncertainties and results in a final definition of plasmid and chromosome content.