POPULATION SEQUENCING USING SHORT READ TECHNOLOGIES
First Claim
1. A system that enables generating population sequences based on short reads, comprising:
- a read generation component that obtains short reads from a sample that includes a plurality of strain variants; and
a reconstruction component that combines the short reads to generate sequenced genomes associated with the plurality of strain variants in the sample and relative concentrations of the strain variants in the sample.
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Accused Products
Abstract
The claimed subject matter provides systems and/or methods that facilitate generating population sequences of strain variants included in a sample. Sequencing can be based on high throughput of short reads. Further, site variants exhibited in the short reads can be linked to reconstruct multiple full strains of a targeted gene, including low concentration variants in the sample. Cues in the short read data can be utilized to perform multi-strain assembly. For example, the cues can include different strain concentrations that lead to more frequently seen strains being responsible for more frequent reads and quilting of overlapping reads to infer mutation linkage over long stretches of DNA.
11 Citations
20 Claims
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1. A system that enables generating population sequences based on short reads, comprising:
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a read generation component that obtains short reads from a sample that includes a plurality of strain variants; and a reconstruction component that combines the short reads to generate sequenced genomes associated with the plurality of strain variants in the sample and relative concentrations of the strain variants in the sample. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12)
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13. A method that facilitates sequencing multiple variants included in a mixed sample, comprising:
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obtaining a set of short reads based upon a sample that includes a plurality of varying strains; determining an identity of a strain and a location within the identified strain corresponding to each short read in the set; and reconstructing sequences of the plurality of varying strains from the set of short reads based upon the strain identity and location related to each short read in the set. - View Dependent Claims (14, 15, 16, 17, 18, 19)
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20. A system that enables sequencing a plurality of variants included in a mixed sample, comprising:
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means for determining respective strain identities corresponding to a plurality of short reads; means for recognizing respective locations within the identified strains covered by each of the plurality of short read; and means for assembling the plurality of short reads to reconstruct sequences of a plurality of strain variants based upon the respective strain identities and respective locations.
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Specification