A computer-implemented method for onsite or cloud-based DNA or RNA processing and analysis, the method comprising: providing a platform application programming interface defining an input for receiving result data from a secondary processing of a plurality of reads of DNA, RNA or genomic sequence data from a subject, providing a bioinformatics processing platform having a memory that stores one or more DNA or RNA reference sequences, and having an integrated circuit formed of a set of pre-configured hardwired digital logic circuits that are interconnected by a plurality of physical electrical interconnects, the integrated circuit having an input for receiving a plurality of reads of DNA or RNA data, and having a memory interface to access the one or more DNA or RNA reference sequences, the hardwired digital logic circuits being arranged as a set of processing engines that are each formed of a subset of the hardwired digital logic circuits to perform one pre-configured step of secondary processing on the plurality of reads of DNA or RNA data, wherein secondary processing comprises receiving the plurality of reads of genomic sequence data and one or more DNA or RNA reference sequences and processing the plurality of reads of genomic sequence data to map and align at least some of the plurality of reads of genomic sequence data according to the one or more DNA or RNA reference sequences, the integrated circuit further having an output to output result data from the secondary processing according to the platform application programming interface, wherein the integrated circuit is physically integrated with an automated sequencer; and providing a plurality of user-selectable DNA, RNA or genomic processing pipelines, each having an input defined according to the platform API to receive the result data from the secondary processing, the plurality of DNA, RNA or genomic processing pipelines having a common pipeline API defining tertiary processing operations on the result data from the secondary processing received according to the platform API, wherein tertiary processing comprises performing one or more analyses on the subject's genetic makeup determined by the secondary processing and each of the plurality of DNA, RNA or genomic processing pipelines is configured to perform a subset of the tertiary processing operations, and executing a user-selected set of the DNA, RNA or genomic processing pipelines, wherein the user-selected set of the DNA, RNA or genomic processing pipelines are configured to output result data of the tertiary processing according to the pipeline API to one or more user-selectable DNA, RNA or genomic analysis applications for additional processing for disease diagnostic, therapeutic treatment and/or prophylactic prevention. providing a platform application programming interface defining an input for receiving result data from a secondary processing of a plurality of reads of DNA, RNA or genomic sequence data from a subject, providing a bioinformatics processing platform having a memory that stores one or more DNA or RNA reference sequences, and having an integrated circuit formed of a set of pre-configured hardwired digital logic circuits that are interconnected by a plurality of physical electrical interconnects, the integrated circuit having an input for receiving a plurality of reads of DNA or RNA data, and having a memory interface to access the one or more DNA or RNA reference sequences, the hardwired digital logic circuits being arranged as a set of processing engines that are each formed of a subset of the hardwired digital logic circuits to perform one pre-configured step of secondary processing on the plurality of reads of DNA or RNA data, wherein secondary processing comprises receiving the plurality of reads of genomic sequence data and one or more DNA or RNA reference sequences and processing the plurality of reads of genomic sequence data to map and align at least some of the plurality of reads of genomic sequence data according to the one or more DNA or RNA reference sequences, the integrated circuit further having an output to output result data from the secondary processing according to the platform application programming interface, wherein the integrated circuit is physically integrated with an automated sequencer; and providing a plurality of user-selectable DNA, RNA or genomic processing pipelines, each having an input defined according to the platform API to receive the result data from the secondary processing, the plurality of DNA, RNA or genomic processing pipelines having a common pipeline API defining tertiary processing operations on the result data from the secondary processing received according to the platform API, wherein tertiary processing comprises performing one or more analyses on the subject's genetic makeup determined by the secondary processing and each of the plurality of DNA, RNA or genomic processing pipelines is configured to perform a subset of the tertiary processing operations, and executing a user-selected set of the DNA, RNA or genomic processing pipelines, wherein the user-selected set of the DNA, RNA or genomic processing pipelines are configured to output result data of the tertiary processing according to the pipeline API to one or more user-selectable DNA, RNA or genomic analysis applications for additional processing for disease diagnostic, therapeutic treatment and/or prophylactic prevention.