Enhanced amplicon sequencing analysis

Abstract

An Amplicon Sequencing Analysis Pipeline (ASAP) system (120, 600) characterizes a genetic sample. The ASAP system (120, 600) receives assay configuration data individually associating reference sequences and genetic characteristics. The ASAP system (120, 600) processes amplicon sequencing data and the reference sequences to characterize the genetic sample based on the individual associations between the reference sequences and the genetic characteristics in the assay configuration data. The ASAP (120, 600) system transfers genetic data indicating the genetic characteristics for the genetic sample and indicating interpretation metrics for amplicon sequencing read depth and quality related to the genetic characteristics.

What is claimed is: 
     
         1 . A method of operating an Amplicon Sequencing Analysis Pipeline (ASAP) system to characterize a genetic sample, the method comprising receiving assay configuration data to characterize the genetic sample, the method characterized by:
 receiving the assay configuration data that individually associates reference sequences with genetic characteristics and that specifies target genetic characteristics;   processing amplicon sequencing data and the reference sequences for the genetic characteristics to identify ones of the reference sequences;   processing the identified ones of the reference sequences and the individual associations between the reference sequences and the genetic characteristics to identify a presence of the target genetic characteristics in genetic sample; and   transferring genetic data indicating the presence of the target genetic characteristics in the genetic sample and indicating interpretation metrics for amplicon sequencing read depth and quality related to the presence of the target genetic characteristics.   
     
     
         2 . The method of  claim 1  wherein the target genetic characteristics comprise an antibiotic resistance for a microbial species. 
     
     
         3 . The method of  claim 1  wherein the target genetic characteristics comprise a virulence factor for a microbial species. 
     
     
         4 . The method of  claim 1  wherein the target genetic characteristics comprise a strain for a genetic species. 
     
     
         5 . The method of  claim 1  wherein the target genetic characteristics comprise a haploid type for a genetic species. 
     
     
         6 . The method of  claim 1  wherein the target genetic characteristics comprise Single Nucleotide Polymorphisms (SNPs) for a genetic species. 
     
     
         7 . The method of  claim 1  wherein the target genetic characteristics comprise species identify for a genetic species. 
     
     
         8 . An Amplicon Sequencing Analysis Pipeline (ASAP) system to characterize a genetic sample comprising a user interface, a processing system, and a communication interface, the ASAP system characterized by:
 the user interface configured to receive assay configuration data that individually associates reference sequences with genetic characteristics and that specifies target genetic characteristics;   the processing system configured to process amplicon sequencing data for the genetic sample and the reference sequences to identify ones of the reference sequences;   the processing system configured to process the identified ones of the reference sequences and the individual associations between the reference sequences and the genetic characteristics to identify a presence of the target genetic characteristics in the genetic sample;   the processing system configured to generate genetic data indicating the presence of the target genetic characteristics and indicating interpretation metrics for amplicon sequencing read depth and quality related to the presence of the target genetic characteristics; and   the communication interface configured to transfer the genetic data.   
     
     
         9 . The ASAP system of  claim 8  wherein the target genetic characteristics comprise an antibiotic resistance for a microbial species. 
     
     
         10 . The ASAP system of  claim 8  wherein the target genetic characteristics comprise a virulence factor for a microbial species. 
     
     
         11 . The ASAP system of  claim 8  wherein the target genetic characteristics comprise a strain for a genetic species. 
     
     
         12 . The ASAP system of  claim 8  wherein the target genetic characteristics comprise a haploid type for a genetic species. 
     
     
         13 . The ASAP system of  claim 8  wherein the target genetic characteristics comprise Single Nucleotide Polymorphisms (SNPs) for a genetic species. 
     
     
         14 . The ASAP system of  claim 8  wherein the target genetic characteristics comprise species identify for a genetic species. 
     
     
         15 . An Amplicon Sequencing Analysis Pipeline (ASAP) computer apparatus to characterize a genetic sample, the ASAP computer apparatus comprising data processing circuitry and at least one or more non-transitory computer-readable storage medium, the computer apparatus characterized by:
 assay software configured to direct the data processing circuitry to process amplicon sequencing data for the genetic sample and assay configuration data that indicates target genetic characteristics and that individually associates reference sequences with genetic characteristics to identify ones of the reference sequences;   the assay software configured to direct the data processing circuitry to process the identified ones of the reference sequences and the individual associations between the reference sequences and the genetic characteristics to identify a presence of the target genetic characteristics in the genetic sample;   alignment software configured to direct the data processing circuitry to generate genetic data indicating the presence of the target genetic characteristics in the genetic sample and indicating interpretation metrics for amplicon sequencing read depth and quality related to the presence of the target genetic characteristics; and   the at least one non-transitory computer-readable storage medium storing the assay software and the alignment software.   
     
     
         16 . The ASAP computer apparatus of  claim 15  wherein the target genetic characteristics comprise an antibiotic resistance for a microbial species. 
     
     
         17 . The ASAP computer apparatus of  claim 15  wherein the target genetic characteristics comprise a virulence factor for a microbial species. 
     
     
         18 . The ASAP computer apparatus of  claim 15  wherein the target genetic characteristics comprise a strain for a genetic species. 
     
     
         19 . The ASAP computer apparatus of  claim 15  wherein the target genetic characteristics comprise a haploid type for a genetic species. 
     
     
         20 . The ASAP computer apparatus of  claim 15  wherein the target genetic characteristics comprise Single Nucleotide Polymorphisms (SNPs) for a genetic species.