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US 11,667,965 B2Granted
Sequence assembly
AssigneeInvitae Corporation
InventorsGregory Porreca, Caleb Kennedy
Life of this patent
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Abstract
The invention relates to assembly of sequence reads. The invention provides a method for identifying a mutation in a nucleic acid involving sequencing nucleic acid to generate a plurality of sequence reads. Reads are assembled to form a contig, which is aligned to a reference. Individual reads are aligned to the contig. Mutations are identified based on the alignments to the reference and to the contig.
Claims20
A method comprising:
- receiving, onto a memory, a plurality of sequence reads from nucleic acid from a sample organism;
- assembling the plurality of sequence reads into an assembly that represents a contiguous region of the nucleic acid;
- aligning the assembly to a reference genome to generate an assembly-reference alignment;
- identifying a plurality of variants in the assembly relative to the reference genome;
- aligning, by pairwise alignment, each of the plurality of sequence reads to the assembly to generate a read-assembly alignment;
- and
- assigning a variant state for each of the plurality of variants relative to the reference genome based on the assembly-reference alignment and the read-assembly alignment to determine genotype information for the sample organism.
4 more elements
A method for genotyping nucleic acids, the method comprising:
- obtaining a sample comprising nucleic acid;
- sequencing the nucleic acid to generate a plurality of sequence reads;
- and
- detecting a variant in the plurality of sequence reads relative to a reference genome, the detecting comprising the steps of:
- assembling a contig from the plurality of sequence reads;
- aligning the contig to the reference genome to obtain a contig-to-reference alignment, the contig-to-reference alignment comprising a position of the contig relative to the reference genome and a description of one or more differences in the aligned contig relative to the reference genome;
- aligning each of the plurality of sequence reads to the aligned contig to obtain a plurality of read-to-contig alignments, the plurality of read-to-contig alignments comprising, for each of the plurality of sequence reads, a position of the sequence read relative to the aligned contig and a description of one or more differences in the aligned sequence read relative to the aligned contig;
- aligning the contig-to-reference alignment to the plurality of read-to-contig alignments to obtain a plurality of read-to-reference alignments, the plurality of read-to-reference alignments comprising, for one or more of the plurality of sequence reads, a position of the one or more of the plurality of sequence reads relative to the reference genome and a description of a difference in the one or more plurality of sequence reads relative to the reference genome;
- and
- outputting the difference as the detected variant.
7 more elements
Dependencies are inferred from the claim text.