Systems and methods for visualizing structural variation and phasing information

A system for providing structural variation and phasing information, the system comprising one or more microprocessors, a persistent memory and a non-persistent memory that collectively store one or more programs that use the one or more microprocessors to perform a method of:

• obtaining a request for structural variation and phasing information in a nucleic acid sequencing dataset, wherein
• the request for structural variation and phasing information in a nucleic acid sequencing dataset is in the form X1:N1-N2,
• X1 is an identity of a selected chromosome or a selected first contig sequence,
• N1 is a selected start position within the first chromosome or the selected first contig sequence,
• N2 is a selected end position within the first chromosome or the selected first contig sequence,
• the nucleic acid sequencing dataset represents at least one target nucleic acid in a sample associated with a genome of a species,
• the nucleic acid sequencing dataset comprises (i) a header, (ii) a synopsis, and (iii) a data section,
• the data section comprises a plurality of sequencing reads organized into a plurality of chunks
• the synopsis includes an identification of a genomic region represented by each chunk in the plurality of chunks,
• each respective sequencing read in the plurality of sequencing reads comprises a nucleic acid sequence comprising a first portion that corresponds to a subset of a target nucleic acid in the at least one target nucleic acid and a second portion that encodes a respective identifier for the respective sequencing read in a plurality of identifiers,
• each respective identifier is independent of each sequence of the at least one target nucleic acid,
• the plurality of sequencing reads collectively include the plurality of identifiers, and
• the nucleic acid sequence dataset is 1 gigabyte or greater in size;
• responsive to obtaining the request, automatically parsing the request by:
• (i) loading the header and the synopsis of the nucleic acid sequencing dataset into the non-persistent memory if not already loaded into the non-persistent memory while retaining the data section in persistent memory,
• (ii) comparing the request to the synopsis of the nucleic acid sequencing dataset thereby identifying from the synopsis one or more chunks in the plurality of chunks of the data section containing variant call data from a range defined by the selected start position and the selected end position,
• (iii) loading the one or more chunks into non-persistent memory, wherein the loading loads less than the entirety of the data section,
• (iv) obtaining structural variation and phasing information for the range or the particular gene within the genome specified by the request from the one or more chunks, and
• (v) formatting the structural variation and phasing information, for the range or for the particular gene, for display using the nucleic acid sequencing dataset.

A system for providing structural variation and phasing information, the system comprising one or more microprocessors, a persistent memory and a non-persistent memory that collectively store one or more programs that use the one or more microprocessors to perform a method of:

• obtaining a request for structural variation and phasing information in a nucleic acid sequencing dataset, wherein
• the request for structural variation and phasing information in a nucleic acid sequencing dataset is in the form X1:N1-N2,
• X1 is an identity of a selected chromosome or a selected first contig sequence,
• N1 is a selected start position within the first chromosome or the selected first contig sequence,
• N2 is a selected end position within the first chromosome or the selected first contig sequence,
• the nucleic acid sequencing dataset represents at least one target nucleic acid in a sample associated with a genome of a species,
• the nucleic acid sequencing dataset comprises (i) a header, (ii) a synopsis, and (iii) a data section,
• the data section comprises a plurality of sequencing reads organized into a plurality of chunks,
• the synopsis includes an identification of a genomic region represented by each chunk in the plurality of chunks,
• each respective sequencing read in the plurality of sequencing reads comprises a nucleic acid sequence comprising a first portion that corresponds to a subset of a target nucleic acid in the at least one target nucleic acid and a second portion that encodes a respective identifier for the respective sequencing read in a plurality of identifiers, each respective identifier is independent of each sequence of the at least one target nucleic acid,
• the plurality of sequencing reads collectively include the plurality of identifiers, and
• the nucleic acid sequence dataset is 1 gigabyte or greater in size;
• responsive to obtaining the request, automatically parsing the request by:
• (i) loading the header and the synopsis of the nucleic acid sequencing dataset into the non-persistent memory if not already loaded into the non-persistent memory while retaining the data section in persistent memory,
• (ii) comparing the request to the synopsis of the nucleic acid sequencing dataset thereby identifying from the synopsis one or more chunks in the plurality of chunks of the data section containing variant call data from a range defined by the selected start position and the selected end position,
• (iii) loading the one or more chunks into non-persistent memory, wherein the loading loads less than the entirety of the data section,
• (iv) obtaining structural variation and phasing information for the range, and
• (v) formatting the structural variation and phasing information, for the range, for display using the nucleic acid sequencing dataset.

A system for providing structural variation and phasing information, the system comprising one or more microprocessors, a persistent memory and a non-persistent memory that collectively store one or more programs that use the one or more microprocessors to perform a method of:

• obtaining a request for structural variation and phasing information in a nucleic acid sequencing dataset, wherein
• the request for structural variation and phasing information in a nucleic acid sequencing dataset is in the form Y1, Y2, . . . , YN,
• each Yi in Y1, Y2, . . . , YN is either an alphanumeric identification of a selected gene, a selection of a chromosomal region, or selection of a region of a contig sequence,
• the nucleic acid sequencing dataset comprises (i) a header, (ii) a synopsis, and (iii) a data section,
• the data section comprises a plurality of sequencing reads organized into a plurality of chunks,
• the synopsis includes an identification of a genomic region represented by each chunk in the plurality of chunks,
• each respective sequencing read in the plurality of sequencing reads comprises a nucleic acid sequence comprising a first portion that corresponds to a subset of a target nucleic acid in the at least one target nucleic acid and a second portion that encodes a respective identifier for the respective sequencing read in a plurality of identifiers,
• each respective identifier is independent of each sequence of the at least one target nucleic acid,
• the plurality of sequencing reads collectively include the plurality of identifiers, and
• the nucleic acid sequence dataset is 1 gigabyte or greater in size;
• responsive to obtaining the request, automatically parsing the request by:
• (i) loading the header and the synopsis of the nucleic acid sequencing dataset into the non-persistent memory if not already loaded into the non-persistent memory while retaining the data section in persistent memory,
• (ii) comparing the request to the synopsis of the nucleic acid sequencing dataset thereby identifying from the synopsis one or more chunks in the plurality of chunks of the data section containing variant call data of the selected gene, chromosomal region, or region of the contig sequence,
• (iii) loading the one or more chunks into non-persistent memory, wherein the loading loads less than the entirety of the data section,
• (iv) obtaining structural variation and phasing information for the selected gene, chromosomal region, or region of the contig sequence, and
• (v) formatting the structural variation and phasing information, for the selected gene, chromosomal region, or region of the contig sequence, for display using the nucleic acid sequencing dataset.

A method for providing structural variation and phasing information, the method comprising:

• obtaining a request for structural variation and phasing information in a nucleic acid sequencing dataset, wherein
• the nucleic acid sequencing dataset represents at least one target nucleic acid in a sample associated with a genome of a species,
• the nucleic acid sequencing dataset comprises (i) a header, (ii) a synopsis, and (iii) a data section,
• the data section comprises a plurality of sequencing reads organized into a plurality of chunks,
• the synopsis includes an identification of a genomic region represented by each chunk in the plurality of chunks,
• each respective sequencing read in the plurality of sequencing reads comprises a nucleic acid sequence comprising a first portion that corresponds to a subset of a target nucleic acid in the at least one target nucleic acid and a second portion that encodes a respective identifier for the respective sequencing read in a plurality of identifiers,
• each respective identifier is independent of each sequence of the at least one target nucleic acid,
• the plurality of sequencing reads collectively include the plurality of identifiers, and
• the nucleic acid sequence dataset is 1 gigabyte or greater in size;
• responsive to obtaining the request for structural variation and phasing information in a range within the genome or for a particular gene, automatically parsing the request at a computer system comprising a processor, non-persistent memory, and persistent memory, by:
• (i) loading the header and the synopsis of the nucleic acid sequencing dataset into the non-persistent memory if not already loaded into the non-persistent memory while retaining the data section in persistent memory,
• (ii) comparing the request to the synopsis of the nucleic acid sequencing dataset thereby identifying from the synopsis one or more chunks in the plurality of chunks of the data section containing variant call data form the range of the request or the particular gene of the request,
• (iii) loading the one or more chunks into non-persistent memory, wherein the loading loads less than the entirety of the data section, (iv) obtaining structural variation and phasing information for the range or the particular gene within the genome specified by the request from the one or more chunks, and
• (v) formatting the structural variation and phasing information, for the range or for the particular gene, for display, wherein the displayed structural variation and phasing information includes an allele for a structural variant and a number of identifiers in the plurality of identifiers that are associated with the allele for the structural variant.

A non-transitory computer readable storage medium for providing structural variation and phasing information, wherein the non-transitory computer readable storage medium stores instructions, which when executed by a computer system comprising non-persistent memory and persistent memory, cause the computer system to perform a method comprising:

• obtaining a request for structural variation and phasing information in a nucleic acid sequencing dataset, wherein
• the nucleic acid sequencing dataset represents at least one target nucleic acid in a sample associated with a genome of a species,
• the data section comprises a plurality of sequencing reads organized into a plurality of chunks,
• the synopsis includes an identification of a genomic region represented by each chunk in the plurality of chunks,
• each respective sequencing read in the plurality of sequencing reads comprises a nucleic acid sequence comprising a first portion that corresponds to a subset of a target nucleic acid in the at least one target nucleic acid and a second portion that encodes a respective identifier for the respective sequencing read in a plurality of identifiers,
• each respective identifier is independent of each sequence of the at least one target nucleic acid,
• the plurality of sequencing reads collectively include the plurality of identifiers, and
• the nucleic acid sequence dataset is 1 gigabyte or greater in size;
• responsive to obtaining the request for structural variation and phasing information in a range within the genome or for a particular gene, automatically parsing the request at a computer system comprising a processor, non-persistent memory, and persistent memory, by:
• (i) loading the header and the synopsis of the nucleic acid sequencing dataset into the non-persistent memory if not already loaded into the non-persistent memory while retaining the data section in persistent memory,
• (ii) comparing the request to the synopsis of the nucleic acid sequencing dataset thereby identifying from the synopsis one or more chunks in the plurality of chunks of the data section containing variant call data form the range of the request or the particular gene of the request,
• (iii) loading the one or more chunks into non-persistent memory, wherein the loading loads less than the entirety of the data section,
• (iv) obtaining structural variation and phasing information for the range or the particular gene within the genome specified by the request from the one or more chunks, and
• (v) formatting the structural variation and phasing information, for the range or for the particular gene, for display, wherein the displayed structural variation and phasing information includes an allele for a structural variant and a number of identifiers in the plurality of identifiers that are associated with the allele for the structural variant.