Patent ID: 11923049
Assignee: SOPHIA GENETICS S.A.
Field: Computer technology (Electrical engineering)
Classification: CPC G | IPC G

Claim 0:
1. A computer-implemented method to analyze next generation sequencing genomic data from a sourcing laboratory, comprising:
receiving, with a processor, via a communication network, a next generation sequencing analysis request from a sourcing laboratory, the next generation sequence request generated via a laboratory computing infrastructure of the sourcing laboratory, the next generation sequencing request comprising at least a raw sequencing data file and a sourcing laboratory identification;
identifying, with a processor, a first set of characteristics associated with the next generation sequencing analysis request, 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 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 raw sequencing data to a genomic sequence to produce a raw alignment file;
identifying, with a processor, a second set of characteristics associated with the alignment data 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 raw alignment data to produce a refined alignment data file,
wherein refining the subset of the input raw alignment data to produce the refined alignment data file comprises re-aligning a subset of the raw alignment data file;
configuring, with a processor, a variant calling module to identify variants associated with the raw sequencing data file in accordance with at least one characteristic of said first set of characteristics and at least one characteristic of the second set of characteristics; and
identifying genomic variants, with the variant calling module processor, in the refined alignment data file.