Systems and methods for data communication, storage, and analysis using reference motifs
Systems and methods for communicating, storing, and/or analyzing data that may include genomic data are described herein. In various embodiments, unaligned genomic sequence read data and/or portions thereof may be stored and/or communicated as a list of variants relative to a particular reference associated with a reference motif identified in the genomic sequence read data. In further embodiments, quality score information associated with a genomic dataset may be analyzed and/or communicated as quality score parameter information. Additional embodiments may facilitate relatively efficient analysis of unaligned genomic sequence read data using metadata associated with reference motifs identified in the unaligned genomic sequence read data.
1. A method for efficiently communicating genomic information, comprising:
providing, by a second computing system to a first computing system, a request to transfer unaligned genomic sequence read data and associated quality score information to the second computing system;
receiving, from the first computer system, a response to the request comprising a variant list, one or more indications of first and second reference motifs, and quality score curve parameter information:
the variant list indicating differences between at least a first portion of the unaligned genomic sequence read data and at least a portion of a first reference sequence and differences between at least a second portion of the unaligned genomic sequence read data and at least a portion of a second reference sequence, the variant list being generated based on a comparison between the first portion of the unaligned genomic sequence read data and the at least a portion of the first reference sequence, and a comparison between the second portion of the unaligned genomic sequence read data and the at least a portion of the second reference sequence:
the second reference sequence being selected from a reference table, the second reference sequence being associated with a second reference motif, the second reference motif identified as being included in the unaligned genomic sequence read data and being different than a first reference motif;
the first reference sequence being selected from the reference table, the first reference sequence being associated with the first reference motif, the first reference motif identified as being included in the unaligned genomic sequence read data; and
the reference table comprising a plurality of reference motifs and a plurality of reference sequences, wherein each reference motif of the plurality of reference motifs is associated with a reference sequence of the plurality of reference sequences; and
the quality score curve parameter information being generated based on a quality score curve, the quality score curve parameter information characterizing the quality score curve:
the quality score curve being generated based on the quality score information, the quality score information being associated with the unaligned genomic sequence read data;
reconstructing, by the second computing system, the unaligned genomic sequence read data based on the variant list and the one or more indications of first and second reference motifs without transferring the unaligned genomic sequence read data to the second computing system; and
reconstructing, by the second computing system, at least an approximation of the quality score curve based on the quality score curve parameter information without transferring the quality score information associated with the unaligned genomic sequence read data to the second computing system.
2. The method of claim 1 , wherein the reference table comprises a locally-stored reference table managed by the first computing system, the locally-stored reference table accessed to identify the first and second reference motifs.
3. The method of claim 1 , wherein the reference table comprises a remotely-stored reference table, the remotely-stored reference table accessed from a third-party service to identify the first and second reference motifs.
4. The method of claim 1 , wherein the indication of the first and second reference motifs comprises a first pointer to the at least a portion of the first reference sequence and a second pointer to the at least a portion of the second reference sequence.
5. The method of claim 1 , wherein the quality score curve parameter information comprises-polynomial coefficients associated with a polynomial approximation of the quality score curve.
6. The method of claim 1 , wherein the quality score parameter information comprises-parameters associated with a trigonometric approximation of the quality score curve.
7. The method of claim 6 , wherein the trigonometric approximation comprises a sinusoidal approximation.
8. The method of claim 1 , wherein the quality score parameter information comprises indications of differences between the quality score curve and at least one of one or more reference quality score curves.
9. The method of claim 8 , wherein the indications of differences between the quality score curve and at least one of the one or more reference quality score curves comprise at least one predefined difference.
10. The method of claim 1 , further comprising receiving the quality score curve by the second computer system.