Automated systems and methods for pathogen identification

A computer implemented method for designing a diagnostic assay for one or more target agents, the method comprising:

• a) determining nucleic acid molecular identifiers for the one or more target agents;
• b) designing an amplification primer set for one or more nucleic acid molecular identifiers;
• c) generating one or more collections of amplification primer sets for all of the one or more target agents;
• d) classifying each of the one or more collections of amplification primer sets according to their collective distinguishing power in a putative amplification assay for identifying and distinguishing any one or more or all of the one or more target agents;
• and
• e) validating at least one of the one or more collections of amplification primer sets in an amplification assay,
• wherein any one or more or all of steps a-d are carried out with an artificial intelligence and machine learning (AI/ML) system.