Sequence assembly
AssigneeLaboratory Corporation of America Holdings
InventorsGregory Porreca, Caleb J. 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.
Claims21
-12. (canceled)
A method for assembling nucleotide data sequences, the method comprising:
- obtaining nucleotide data sequences, the obtaining comprising sequencing a sample that comprises a template nucleic acid;
- and
- inputting a reference genome and the nucleotide data sequences into a computer system comprising a processor coupled to a non-transitory memory to perform:
- assembling a contig using at least some of the nucleotide data sequences;
- identifying a plurality of contig:reference descriptions by aligning the contig to the reference genome;
- identifying a plurality of read:contig descriptions by aligning multiple ones of the nucleotide data sequences to the contig;
- and
- combining the plurality of contig:reference descriptions with the plurality of read:contig descriptions to produce read:reference descriptions that map positional information of mutations found in the individual ones of the nucleotide data sequences relative to the reference genome.
A method for assembling nucleotide data sequences, the method comprising using a computer hardware processor to perform:
- obtaining nucleotide data sequences previously generated by a process comprising sequencing a sample that comprises a template nucleic acid;
- assembling a contig using at least some of the nucleotide data sequences;
- identifying a plurality of contig:reference descriptions by aligning the contig to a reference genome;
- identifying a plurality of read:contig descriptions by aligning multiple ones of the nucleotide data sequences to the contig;
- and
- combining the plurality of contig:reference descriptions with the plurality of read:contig descriptions to produce read:reference descriptions that map positional information of mutations found in the individual ones of the nucleotide data sequences relative to the reference genome.
Dependencies are inferred from the claim text.