Systems and methods for smart tools in sequence pipelines
First Claim
1. A system for genomic analysis, the system comprising:
- a processor coupled to a memory operable to cause the system to;
present to a user a plurality of genomic tools organized into a bioinformatics pipeline, wherein at least a first one of the genomic tools comprises an executable and a wrapper script;
receive instructions from the user and sequence data, wherein the instructions call for the sequence data to be analyzed by the bioinformatics pipeline;
initiate the executable of the first genomic tool of the bioinformatics pipeline; and
modify, using the wrapper script, the bioinformatics pipeline to replace the first genomic tool of the bioinformatics pipeline with an alternative genomic tool, wherein the wrapper script modifies the bioinformatics pipeline by;
receiving an error from the executable of the first genomic tool;
identifying the alternative genomic tool that is consistent with the user instructions and the data being passed; and
initiating an executable of the alternative genomic tool, wherein the alternative genomic tool avoids the error.
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Accused Products
Abstract
A tool in a bioinformatics pipeline can include a smart wrapper and an executable. The smart wrapper can cause the executable to analyze the sequence data it receives and can also selectively change to the pipeline when circumstances warrant. In certain aspects, a system for genomic analysis includes a processor coupled to a non-transitory memory. The system is operable to present to a user a plurality of genomic tools organized into a pipeline. At least a first one of the tools comprises an executable and a wrapper script. The system can receive instructions from the user and sequence data—instructions that call for the sequence data to be analyzed by the pipeline—and select, using the wrapper script, a change to the pipeline.
83 Citations
20 Claims
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1. A system for genomic analysis, the system comprising:
a processor coupled to a memory operable to cause the system to; present to a user a plurality of genomic tools organized into a bioinformatics pipeline, wherein at least a first one of the genomic tools comprises an executable and a wrapper script; receive instructions from the user and sequence data, wherein the instructions call for the sequence data to be analyzed by the bioinformatics pipeline; initiate the executable of the first genomic tool of the bioinformatics pipeline; and modify, using the wrapper script, the bioinformatics pipeline to replace the first genomic tool of the bioinformatics pipeline with an alternative genomic tool, wherein the wrapper script modifies the bioinformatics pipeline by; receiving an error from the executable of the first genomic tool; identifying the alternative genomic tool that is consistent with the user instructions and the data being passed; and initiating an executable of the alternative genomic tool, wherein the alternative genomic tool avoids the error. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19)
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20. A system for genomic analysis, the system comprising:
a processor coupled to a memory operable to cause the system to; present to a user one or more bioinformatics pipelines for genomic analysis, the bioinformatics pipelines comprising a plurality of genomic tools each comprising an executable and a wrapper script; receive instructions from the user to process sequence data using a selected bioinformatics pipeline of genomic tools; initiate the executable of a first genomic tool of the selected bioinformatics pipeline; and modify, using the wrapper script, the bioinformatics pipeline to replace the first genomic tool of the bioinformatics pipeline with an alternative genomic tool, wherein the wrapper script modifies the bioinformatics pipeline by; receiving an error from the executable of the first genomic tool; identifying the alternative genomic tool that is consistent with the user instructions and the data being passed; and running an executable of the alternative genomic tool, wherein the alternative tool avoids the error.
Specification