Patent ID: 11915797
Assignee: GRAIL, INC.
Field: Computer technology (Electrical engineering)
Classification: CPC G | IPC G

Claim 0:
1. A method for determining support characteristics of positions across a reference genome, the method comprising:
accessing a reference genome sequence expressed in a first format that represents each nucleotide base as a character using a full byte;
accessing a sequence read expressed in a second format that represents each nucleotide base as a numerical value using half a byte;
converting the first format of the reference genome sequence into an internal representation which represents each nucleotide base as a numerical value using a full byte;
converting the second format of the sequence read into the internal representation, wherein the converting comprises:
loading the sequence read into a 16-byte array;
extracting nucleotide bases at even positions and nucleotide bases at odd positions of the sequence read from the 16-byte array using a 16-byte mask;
unpacking and interleaving a lower half of the nucleotide bases at even positions and a lower half of the nucleotide bases at odd positions as first 16 bytes;
unpacking and interleaving a higher half of the nucleotide bases at even positions and a higher half of the nucleotide bases at odd positions as second 16 bytes; and
reordering the nucleotide bases in the sequence read by storing the first 16 bytes followed by the second 16 bytes into an output array representing the sequence read in the internal representation;

identifying one or more mismatched nucleotide bases by comparing at least N contiguous nucleotide bases of the sequence read expressed in the internal representation to at least N contiguous nucleotide bases of the reference genome sequence expressed in the internal representation, wherein N is greater than 1.