A method to analyze next generation sequencing genomic data from a sourcing laboratory, comprising: - receiving, with a processor, a next generation sequencing analysis request from a sourcing laboratory, the next generation sequencing request comprising at least a raw next generation sequencing data file and the sourcing laboratory identification; - identifying, with a processor, a first set of characteristics associated with the sourcing laboratory identification, the first set of characteristics comprising at least a target enrichment technology identifier, a sequencing technology identifier, and a genomic context identifier; - configuring, with a processor, a data alignment module to align the input raw sequencing data file in accordance with at least one characteristic of said first set of characteristics; - aligning, with the data alignment module processor, the input raw sequencing data to a genomic sequence to produce a raw alignment data file, the method further comprises: - identifying, with a processor, a second set of characteristics from the raw alignment data file, the second set of characteristics comprising at least a data alignment pattern identifier; - configuring, with a processor, the data alignment module to refine at least one subset of the input raw sequencing data in accordance with at least one characteristic of the first set of characteristics and at least one characteristic of the second set of characteristics; - refining with the configured data alignment module processor, the subset of the input raw alignment data to produce a refined alignment data file - configuring, with a processor, a variant calling module to identify variants associated with the input sequencing data in accordance with at least one characteristic of said first set of characteristics and at least one characteristic of the second set of characteristics; - identifying genomic variants, with the variant calling module processor, in the refined alignment data file. - receiving, with a processor, a next generation sequencing analysis request from a sourcing laboratory, the next generation sequencing request comprising at least a raw next generation sequencing data file and the sourcing laboratory identification; - identifying, with a processor, a first set of characteristics associated with the sourcing laboratory identification, the first set of characteristics comprising at least a target enrichment technology identifier, a sequencing technology identifier, and a genomic context identifier; - configuring, with a processor, a data alignment module to align the input raw sequencing data file in accordance with at least one characteristic of said first set of characteristics; - aligning, with the data alignment module processor, the input raw sequencing data to a genomic sequence to produce a raw alignment data file, the method further comprises: - identifying, with a processor, a second set of characteristics from the raw alignment data file, the second set of characteristics comprising at least a data alignment pattern identifier; - configuring, with a processor, the data alignment module to refine at least one subset of the input raw sequencing data in accordance with at least one characteristic of the first set of characteristics and at least one characteristic of the second set of characteristics; - refining with the configured data alignment module processor, the subset of the input raw alignment data to produce a refined alignment data file - configuring, with a processor, a variant calling module to identify variants associated with the input sequencing data in accordance with at least one characteristic of said first set of characteristics and at least one characteristic of the second set of characteristics; - identifying genomic variants, with the variant calling module processor, in the refined alignment data file. - identifying, with a processor, a second set of characteristics from the raw alignment data file, the second set of characteristics comprising at least a data alignment pattern identifier; - configuring, with a processor, the data alignment module to refine at least one subset of the input raw sequencing data in accordance with at least one characteristic of the first set of characteristics and at least one characteristic of the second set of characteristics; - refining with the configured data alignment module processor, the subset of the input raw alignment data to produce a refined alignment data file - configuring, with a processor, a variant calling module to identify variants associated with the input sequencing data in accordance with at least one characteristic of said first set of characteristics and at least one characteristic of the second set of characteristics; - identifying genomic variants, with the variant calling module processor, in the refined alignment data file.