Abstract: Provided herein are fully-automated next-generation sequencing platforms and processes for detection of a target specimen (e.g., SARS-CoV-2) and for distinguishing infectious from non-infectious signals from the specimen. An analysis can provide simultaneous diagnosis and genomic surveillance of a multitude of distinct specimens in a sample information. The analysis can comprise distinguishing between infectious versus infectious specimens and provide a recommendation as to how infectious the sample can be. The information can be used to better inform the status of a subject or a location with regards to infectivity from the specimen.

Abstract: Provided herein are methods and apparatus for the identification of pathogenic and non-pathogenic microorganisms in food and environmental samples. The disclosure solves existing challenges encountered in identifying food borne pathogens, including pathogens of the Salmonella, Campylobacter, Listeria, and Escherichia genera in a timely and efficient manner. The disclosure also provides methods for differentiating a transient versus a resident pathogen, correlating presence of non-pathogenic with pathogenic microorganisms, distinguishing live versus dead microorganisms by sequencing.

Abstract: Aspects of the embodiments use nucleic acid sequence (NS) based barcodes (NS tracking barcodes) in different capacities to track, trace, monitor, optimize, and troubleshoot complex biological, chemical, and biochemical processes. At least two forms of the NS tracking barcodes are described herein: ported NS tracking barcodes and process NS tracking barcodes. Ported NS tracking barcodes are designed such that they will not be modified during the process, and their sequence can indicate time or location of manufacture information, as well as an indication of success of a DNA processing step. Process NS tracking barcodes can be more complicated than the ported NS tracking barcodes, as they can be modified during the course of DNA processing, so that they can provide specific information regarding whether a desired nucleic acid process or reaction worked or did not. Process NS tracking barcodes can be synthesized such that they can used as a substrate for the reaction and get modified.