METHODS FOR GENOME ASSEMBLY, HAPLOTYPE PHASING, AND TARGET INDEPENDENT NUCLEIC ACID DETECTION
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Abstract
The disclosure provides methods for haplotype phasing and meta-genomics assemblies. The disclosure provides a streamlined method for accomplishing these tasks, such that intermediates need not be labeled by an affinity label to facilitate binding to a solid surface. The disclosure also provides methods and compositions for the de novo generation of scaffold information, linkage information, and genome information for unknown organisms in heterogeneous metagenomic samples or samples obtained from multiple individuals. Practice of the methods can allow de novo sequencing of entire genomes of uncultured or unidentified organisms in heterogeneous samples, or the determination of linkage information for nucleic acid molecules in samples comprising nucleic acids obtained from multiple individuals.
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Citations
43 Claims
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1-22. -22. (canceled)
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23. A method of determining genomic linkage information for a heterogeneous nucleic acid sample comprising:
- (a) obtaining a stabilized heterogeneous nucleic acid sample, wherein the stabilized heterogeneous nucleic acid sample comprises a plurality of DNA segments each of the plurality of DNA segments held together independent of their common phosphodiester backbone, wherein the common phosphodiester backbone is cleaved to create exposed DNA ends;
(b) labeling the exposed DNA ends to form labeled exposed DNA ends;
(c) ligating the labeled exposed DNA ends to form labeled paired ends;
(d) sequencing across the labeled paired ends to generate a plurality of paired sequence reads; and
(e) assigning each half of a paired sequence read of the plurality of paired sequence reads to a common nucleic acid molecule of origin. - View Dependent Claims (24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43)
- (a) obtaining a stabilized heterogeneous nucleic acid sample, wherein the stabilized heterogeneous nucleic acid sample comprises a plurality of DNA segments each of the plurality of DNA segments held together independent of their common phosphodiester backbone, wherein the common phosphodiester backbone is cleaved to create exposed DNA ends;
Specification