Fig. 4

Outline of the read-based performance assessment. Plasmidome (I) and metagenome reads (II) are obtained from subsamples of the same sample. (III) The metagenome reads are assembled into a graph. (IV) The graph is used to detect and report plasmids by the algorithm of choice. (V) The plasmidome reads are matched to assembled plasmids. Matched plasmids (red) are used to calculate plasmid read-based precision. (VI) The plasmidome reads are matched to the assembly graph contigs. Covered contigs (red) are considered plasmidic. The fraction of total length of plasmidic contigs included in the detected plasmids gives the plasmidome read-based recall