Fig. 1.

Schematic representation of the metagenomic workflow and quality control steps. The whole process is summarized in the middle. On the left side, internal control (MS2 bacteriophage) is represented in blue, and external controls are represented in red, including positive control (MS2 bacteriophage spiked in viral transport medium) and No-Template Control (NTC: viral transport medium). Quality control testing 1 corresponds to MS2 bacteriophage molecular detection with commercial PCR assay. Quality control testing 2 corresponds to control by sequencing metrics (number of MS2 reads normalized with RPKM ratio and MS2 genome coverage). On the right, each technique used by phases is indicated black. In addition, on the far right the duration of each step is indicated