Genomic infrastructure for on-site or cloud-based DNA and RNA processing and analysis

A system for dynamic configuration and execution of a genomic data processing pipeline based on one or more user-selectable options presented via a graphical user interface (GUI) of a nucleic acid sequencing device, the system comprising:

• a nucleic acid sequencing device that includes one or more processors and one more memory devices storing instructions that, when executed by the one or more processors, cause the one or more processors to perform operations;
• and
• a second device that includes one or more programmable logic devices that can be configured to execute one or more operations on input data obtained by the second device;
• wherein the system is configured to perform operations comprising:
• obtaining, by the one or more processors of the nucleic acid sequencing device executing an application programming interface (API) that provides an interface between the GUI of the nucleic acid sequencing device and a programmable logic device, first data representing a selection of one or more of the user-selectable options submitted via the GUI, wherein one of the user-selectable options identifies a particular reference sequence to be used by a genomic data processing pipeline;
• configuring, by the one or more processors of the nucleic acid sequencing device, one or more programmable hardware resources of the programmable logic device from a first state that does not include hardware resources configured as a genomic analysis pipeline that uses the particular reference sequence identified by the first data into a second state that includes hardware resources that have been configured as a genomic analysis pipeline that uses the particular reference sequence identified by the first data;
• providing, to the programmable logic device and by one or more processors of the nucleic acid sequencing device using the API, second data representing a set of genomic data or a set of data derived from genomic data;
• instructing, by the one or more processors of the nucleic acid sequencing device, the configured genomic data processing pipeline to execute a genomic processing operation on the obtained second data to generate result data;
• obtaining, by the one or more processors of the nucleic acid sequencing device, the result data that is generated by execution of the configured genomic data processing pipeline on the obtained second data by the programmable logic device;
• and
• providing, by the one or more processors of the nucleic acid sequencing device executing one or more of the instructions, output data that is based on the result data.

One or non-transitory more computer readable storage media storing instructions that, when executed by a nucleic acid sequencing device, cause the nucleic acid sequencing device to perform operations for dynamic configuration and execution of a genomic data processing pipeline based on one or more user-selectable options presented via a graphical user interface (GUI) of the nucleic acid sequencing device, the operations comprising:

• obtaining, by one or more processors of the nucleic acid sequencing device executing an application programming interface (API) that provides an interface between the GUI of the nucleic acid sequencing device and a programmable logic device, first data representing a selection of one or more of the user-selectable options submitted via the GUI, wherein one of the user-selectable options identify a particular reference sequence to be used by a genomic data processing pipeline;
• configuring, by one or more processors of the nucleic acid sequencing device, one or more programmable hardware resources of the programmable logic device from a first state that does not include hardware resources configured as a genomic analysis pipeline that uses the particular reference sequence identified by the first data into a second state that includes hardware resources that have been configured as a genomic analysis pipeline that uses the particular reference sequence identified by the first data;
• providing, by one or more processors of the nucleic acid sequencing device, second data representing a set of genomic data or a set of data derived from genomic data;
• and
• instructing, by one or more processors of the nucleic acid sequencing device, the configured genomic data processing pipeline to execute a genomic processing operation on the obtained second data to generate result data;
• obtaining, by one or more processors of the nucleic acid sequencing device, the result data that is generated by execution of the configured genomic data processing pipeline on the obtained second data by the programmable logic device;
• and
• providing, by one or more processors of the nucleic acid sequencing device, output data that is based on the result data.