FIG 1.

Graphical representation of the UltraSEQ pipeline. Reads are optionally preprocessed and aligned to reference databases, and distinct regions within each read are identified. Taxonomy and functional annotations are assigned at the read level and are subsequently combined into sample-level taxonomy profiles by the metagenomics services. The metagenomics diagnostics rules engine (MDRE) service is specific for clinical diagnostics and uses decision trees to identify species and their virulence factors in the sample that cause disease before the reporting of all results. PE, paired end; NN, neural net.