Reference-guided genome sequencing
AssigneeWestern Digital Technologies, Inc.
InventorJustin Kinney
Life of this patent
Estimating the term…
Abstract
Methods and systems for processing a plurality of sample reads for genome sequencing include, for each sample read of the plurality of sample reads, comparing substring sequences from the sample read to reference sequences representing different portions of a reference genome. One or more reference sequences are identified that match one or more of the compared substring sequences, and a probabilistic location within the reference genome is determined for the sample read based on the one or more identified reference sequences. The plurality of sample reads is sorted into a plurality of sample groups based on the determined probabilistic locations of the respective sample reads.
Claims20
A method of processing a plurality of sample reads for genome sequencing using a system comprising at least one systolic array including a plurality of groups of cells, the method comprising:
- for each sample read of the plurality of sample reads:
- comparing substring sequences from the sample read to reference sequences representing different portions of a reference genome, the comparing comprising:
- for each substring sequence from the sample read:
- storing the substring sequence in a first group of cells of the plurality of groups of cells of the at least one systolic array, wherein the first group of cells stores the substring sequence and further stores a first reference sequence;
- comparing the substring sequence stored in the first group of cells to the first reference sequence stored in the first group of cells;
- and
- passing sample values forming the substring sequence from the first group of cells to a second group of cells of the plurality of groups of cells of the at least one systolic array for comparison of the substring sequence to a second reference sequence stored in the second group of cells, wherein the second reference sequence is different from the first reference sequence and the second group of cells does not include any cells of the first group of cells;
- identifying one or more reference sequences stored in one or more groups of cells of the plurality of groups of cells of the at least one systolic array that match one or more substring sequences compared to the one or more reference sequences;
- and
- determining a probabilistic location of the sample read within the reference genome based on the one or more identified reference sequences that match the one or more compared substring sequences;
- and
- sorting the plurality of sample reads into a plurality of sample groups based at least in part on the determined probabilistic locations of the respective sample reads.
A method of operating a system for processing a plurality of sample reads for genome sequencing, wherein the system comprises at least one systolic array including a plurality of groups of cells and a plurality of memories, the method comprising:
- for each sample read of the plurality of sample reads:
- comparing substring sequences from the sample read to reference sequences representing different portions of a reference genome, the comparing comprising:
- for each substring sequence from the sample read:
- storing the substring sequence in the plurality of groups of cells of the at least one systolic array, wherein each group of cells of the plurality of groups of cells stores the substring sequence and further stores a reference sequence that partially overlaps another reference sequence stored in at least one other group of cells of the plurality of groups of cells;
- comparing the substring sequence stored in each group of cells to the reference sequence stored in each group of cells;
- and
- identifying one or more groups of cells of the plurality of groups of cells where the stored reference sequence matches the substring sequence;
- and
- determining a probabilistic location of the sample read within the reference genome based on the one or more identified groups of cells for the substring sequences from the sample read;
- sorting the plurality of sample reads into a plurality of sample groups based at least in part on the determined probabilistic locations of the respective sample reads;
- and
- storing each sample group of the plurality of sample groups in a different memory of the plurality of memories.
A system for processing a plurality of sample reads for genome sequencing, the system comprising:
- at least one systolic array including a plurality of groups of cells;
- a plurality of memories;
- and
- circuitry configured to:
- for each sample read of the plurality of sample reads:
- compare substring sequences from the sample read to reference sequences representing different portions of a reference genome, the comparing comprising:
- for each substring sequence from the sample read:
- store the substring sequence in the plurality of groups of cells of the at least one systolic array, wherein each group of cells of the plurality of groups of cells further stores a reference sequence that partially overlaps another reference sequence stored in at least one other group of cells of the plurality of groups of cells;
- compare the substring sequence stored in each group of cells to the reference sequence stored in each group of cells;
- and
- identify one or more groups of cells of the plurality of groups of cells where the stored reference sequence matches the substring sequence;
- and
- determine a probabilistic location within the reference genome for the sample read based at least in part on the one or more identified groups of cells for the substring sequences from the sample read;
- sort the plurality of sample reads into a plurality of sample groups based on the determined probabilistic locations for the respective sample reads;
- and
- store each sample group of the plurality of sample groups in a different memory of the plurality of memories.
Dependencies are inferred from the claim text.