Genomic infrastructure for on-site or cloud-based DNA and RNA processing and analysis
A system, method and apparatus for executing a sequence analysis pipeline on genetic sequence data includes a integrated circuit formed of a set of hardwired digital logic circuits that are interconnected by physical electrical interconnects. One of the physical electrical interconnects forms an input to the integrated circuit connected with an electronic data source for receiving reads of genomic data. The hardwired digital logic circuits are arranged as a set of processing engines, each processing engine being formed of a subset of the hardwired digital logic circuits to perform one or more steps in the sequence analysis pipeline on the reads of genomic data. Each subset of the hardwired digital logic circuits is formed in a wired configuration to perform the one or more steps in the sequence analysis pipeline.
1. A genomic data analysis platform, the genomic data analysis platform comprising:
a graphical user interface that presents a plurality of user selectable options, with one or more of the plurality of user selectable options corresponding to a particular genomic data processing pipeline; and
a platform application programming interface (API) that
(i) obtains data representing a selection of one or more of the plurality of user selectable options corresponding to a particular genomic data processing pipeline, and
(ii) configures one or more computing resources to implement a set of one or more genomic data processing pipelines based on the obtained data representing the selection, wherein the configuring includes the API defining inputs to each of the one or more genomic data processing pipelines based on the obtained data representing the selection.
2. The genomic data analysis platform in accordance with claim 1 , wherein one or more of the plurality of user selectable options correspond to a particular genomic data analysis application that is stored in one or more application repositories; and
wherein the API further (iii) obtains second data representing a selection of one or more of the plurality of user selectable options corresponding to a particular genomic data analysis application, and (iv) configures one or more inputs to one or more respective genomic data analysis applications stored in the one or more application repositories based on the obtained second data.
3. The genomic data analysis platform in accordance with claim 1 , wherein the plurality of user-selectable options include one or more of a user-selectable option corresponding to a genome processing pipeline, a user-selectable option corresponding to an epigenome processing pipeline, a user-selectable option corresponding to a metagenome processing pipeline, a user-selectable option corresponding to a joint genotyping processing pipeline, or a user-selectable option corresponding to a genome analysis tool kit (GATK) processing pipeline.
4. The genomic data analysis platform in accordance with claim 2 , wherein the plurality of user-selectable options include one or more of a user-selectable option corresponding to a non-invasive prenatal testing application, a user-selectable option corresponding to a neo-natal intensive care unit application, a user-selectable option corresponding to a cancer analysis application, a user-selectable option corresponding to a laboratory developed test (LDT) application, or a user-selectable option corresponding to an agricultural and biological analysis application.
5. A method comprising:
obtaining, by an application programming interface (API) executed by one or more computers, first data representing a selection of one or more of a plurality of user-selectable options submitted via a graphical user interface, wherein one or more of the plurality of user-selectable options identify a particular genomic data processing pipeline;
configuring, using the API executed by the one or more computers, a genomic data processing pipeline based on the first data, wherein configuring the genomic data processing pipeline includes using the API to define inputs to computing resources used to implement each of the one or more genomic data processing pipelines that are identified by the first data;
obtaining, by the one or more computers, second data representing a set of genomic data or a set of data derived from genomic data;
using, by the one or more computers, the genomic data processing pipeline configured based on the first data to process the obtained second data;
obtaining, by the one or more computers, result data that is generated by the genomic data processing pipeline based on the genomic data processing pipeline processing the obtained second data; and
providing, by the one or more computers, output data that is based on the result data.
6. The method of claim 5 , wherein the set of genomic data includes one or more genomic sequences generated by a nucleic acid sequencer.
7. The method of claim 5 , wherein the set of data derived from genomic data includes a set of one or more variants.
8. The method of claim 5 ,
wherein one or more of the plurality of user-selectable options correspond to a particular genomic data analysis application stored in one or more application repositories,
wherein the first data further includes data representing a selection of one or more user-selectable options that each identify one or more genomic data analysis applications, and
wherein the method further comprises:
configuring, by the API, inputs to one or more respective genomic data analysis applications stored in the one or more application repositories based on the obtained first data.
9. The method of claim 5 , wherein the plurality of user-selectable options include one or more of a user-selectable option corresponding to a genome processing pipeline, a user-selectable option corresponding to an epigenome processing pipeline, a user-selectable option corresponding to a metagenome processing pipeline, a user-selectable option corresponding to a joint genotyping processing pipeline, or user-selectable option corresponding to a genome analysis tool kit (GATK) processing pipeline.
10. The method of claim 8 , wherein the plurality of user-selectable options include one or more of a user-selectable option corresponding to a non-invasive prenatal testing application, a user-selectable option corresponding to a neo-natal intensive care unit application, a user-selectable option corresponding to a cancer analysis application, a user-selectable option corresponding to a laboratory developed test (LDT) application, or a user-selectable option corresponding to an agricultural and biological analysis application.
11. A non-transitory computer-readable medium storing software comprising instructions executable by one or more computers which, upon such execution, cause the one or more computers to perform operations comprising:
obtaining, by an application programming interface (API), first data representing a selection of one or more of a plurality of user-selectable options submitted via a graphical user interface, wherein one or more of the plurality of user-selectable options identify a particular genomic data processing pipeline;
configuring, using the API, a genomic data processing pipeline based on the first data, wherein configuring the genomic data processing pipeline includes using the API to define inputs to computing resources used to implement each of the one or more genomic data processing pipelines that are identified by the first data;
obtaining second data representing a set of genomic data or a set of data derived from genomic data;
using the genomic data processing pipeline configured based on the first data to process the obtained second data;
obtaining result data that is generated by the genomic data processing pipeline based on the genomic data processing pipeline processing the obtained second data; and
providing output data that is based on the result data.
12. The computer-readable medium of claim 11 , wherein the set of genomic data includes one or more genomic sequences generated by a nucleic acid sequencer.
13. The computer-readable medium of claim 11 , wherein the set of data derived from genomic data includes a set of one or more variants.
14. The computer-readable medium of claim 11 ,
wherein one or more of the plurality of user-selectable options correspond to a particular genomic data analysis application stored in one or more application repositories,
wherein the first data further includes data representing a selection of one or more user-selectable options that each identify one or more genomic data analysis applications, and
wherein the operations further comprise:
configuring, by the API, inputs to one or more respective genomic data analysis applications stored in the one or more application repositories based on the obtained first data.
15. The computer-readable medium of claim 11 , wherein the plurality of user-selectable options include one or more of a user-selectable option corresponding to a genome processing pipeline, a user-selectable option corresponding to an epigenome processing pipeline, a user-selectable option corresponding to a metagenome processing pipeline, a user-selectable option corresponding to a joint genotyping processing pipeline, or user-selectable option corresponding to a genome analysis tool kit (GATK) processing pipeline.
16. The computer-readable medium of claim 14 , wherein the plurality of user-selectable options include one or more of a user-selectable option corresponding to a non-invasive prenatal testing application, a user-selectable option corresponding to a neo-natal intensive care unit application, a user-selectable option corresponding to a cancer analysis application, a user-selectable option corresponding to a laboratory developed test (LDT) application, or a user-selectable option corresponding to an agricultural and biological analysis application.
17. A system, comprising:
one or more computers and one or more storage devices storing instructions that are operable, when executed by the one or more computers, to cause the one or more computers to perform operations comprising:
obtaining, by an application programming interface (API) hosted by the one or more computers, first data representing a selection of one or more of a plurality of user-selectable options submitted via a graphical user interface, wherein one or more of the plurality of user-selectable options identify a particular genomic data processing pipeline;
configuring, using the API hosted by the one or more computers, a genomic data processing pipeline based on the first data, wherein configuring the genomic data processing pipeline includes using the API to define inputs to computing resources used to implement each of the one or more genomic data processing pipelines that are identified by the first data;
obtaining, by the one or more computers, second data representing a set of genomic data or a set of data derived from genomic data;
using, by the one or more computers, the genomic data processing pipeline configured based on the first data to process the obtained second data;
obtaining result data that is generated by the genomic data processing pipeline based on the genomic data processing pipeline processing the obtained second data; and
providing, by the one or more computers, output data that is based on the result data.
18. The system of claim 17 , wherein the set of genomic data includes one or more genomic sequences generated by a nucleic acid sequencer.
19. The system of claim 17 , wherein the set of data derived from genomic data includes a set of one or more variants.
20. The system of claim 17 ,
wherein one or more of the plurality of user-selectable options correspond to a particular genomic data analysis application stored in one or more application repositories,
wherein the first data further includes data representing a selection of one or more user-selectable options that each identify one or more genomic data analysis applications, and
wherein the operations further comprise:
configuring, by the API, inputs to one or more respective genomic data analysis applications stored in the one or more application repositories based on the obtained first data.
21. The system of claim 17 , wherein the plurality of user-selectable options include one or more of a user-selectable option corresponding to a genome processing pipeline, a user-selectable option corresponding to an epigenome processing pipeline, a user-selectable option corresponding to a metagenome processing pipeline, a user-selectable option corresponding to a joint genotyping processing pipeline, or user-selectable option corresponding to a genome analysis tool kit (GATK) processing pipeline.
22. The system of claim 20 , wherein the plurality of user-selectable options include one or more of a user-selectable option corresponding to a non-invasive prenatal testing application, a user-selectable option corresponding to a neo-natal intensive care unit application, a user-selectable option corresponding to a cancer analysis application, a user-selectable option corresponding to a laboratory developed test (LDT) application, or a user-selectable option corresponding to an agricultural and biological analysis application.