Sequence tag directed subassembly of short sequencing reads into long sequencing reads
First Claim
1. A method for preparing a DNA sequencing library, comprising:
- (a) incorporating at least one first nucleic acid adaptor molecule into at least one member of a target library comprising a plurality of nucleic acid molecules, wherein at least a portion of the first adaptor molecule comprises a first defined sequence;
(b) amplifying the plurality of nucleic acid molecules to produce an input library comprising a first plurality of amplified DNA molecules, wherein the amplified molecules comprise sequence identical to or complementary to at least a portion of the first adaptor molecule and sequence identical to or complementary to at least a portion of at least one member of the target library;
(c) fragmenting the input library to produce a plurality of linear DNA fragments having a first end and a second end;
(d) attaching at least one second nucleic acid adaptor molecule to one or both ends of at least one of the plurality of linear DNA fragments, wherein at least a portion of the second adaptor molecule comprises a second defined sequence; and
(e) amplifying the plurality of linear DNA fragments to produce a sequencing library comprising a second plurality of amplified DNA molecules, wherein at least one of the plurality of amplified DNA molecules comprises sequence identical to or complementary to at least a portion of the first adaptor molecule, sequence identical to or complementary to at least a portion of the second adaptor molecule, and sequence identical to or complementary to at least a portion of a member of the target library.
1 Assignment
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Accused Products
Abstract
The invention provides methods for preparing DNA sequencing libraries for assembling short read sequencing data into longer contiguous sequences and providing for genome assembly, full length cDNA sequencing, metagenomics, and the analysis of repetitive sequences of assembled genomes. The methods generally comprise incorporating adaptor or vector sequences into at least one member of a target fragment library, amplifying the population of target fragment library members to produce a plurality of copies of amplified DNA molecules, fragmenting the plurality of amplified DNA molecules, incorporating additional adaptor sequences, and amplifying a region of at least one of the plurality of amplified DNA molecules. At least one resulting amplicon comprises a sequence identical to or complementary to at least a portion of a sequence tag and a sequence identical to or complementary to a portion of a target fragment library member.
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Citations
28 Claims
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1. A method for preparing a DNA sequencing library, comprising:
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(a) incorporating at least one first nucleic acid adaptor molecule into at least one member of a target library comprising a plurality of nucleic acid molecules, wherein at least a portion of the first adaptor molecule comprises a first defined sequence; (b) amplifying the plurality of nucleic acid molecules to produce an input library comprising a first plurality of amplified DNA molecules, wherein the amplified molecules comprise sequence identical to or complementary to at least a portion of the first adaptor molecule and sequence identical to or complementary to at least a portion of at least one member of the target library; (c) fragmenting the input library to produce a plurality of linear DNA fragments having a first end and a second end; (d) attaching at least one second nucleic acid adaptor molecule to one or both ends of at least one of the plurality of linear DNA fragments, wherein at least a portion of the second adaptor molecule comprises a second defined sequence; and (e) amplifying the plurality of linear DNA fragments to produce a sequencing library comprising a second plurality of amplified DNA molecules, wherein at least one of the plurality of amplified DNA molecules comprises sequence identical to or complementary to at least a portion of the first adaptor molecule, sequence identical to or complementary to at least a portion of the second adaptor molecule, and sequence identical to or complementary to at least a portion of a member of the target library. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17)
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18. A method for preparing a DNA sequencing library, comprising:
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(a) incorporating a first nucleic acid tag adaptor molecule into the first end of at least one linear member of a target library comprising a plurality of linear nucleic acid molecules, wherein at least a portion of the first tag adaptor molecule comprises a first defined tag sequence; (b) incorporating second nucleic acid tag adaptor molecule into the second end of the at least one linear member of the target library, wherein at least a portion of the second tag adaptor molecule comprises a second defined tag sequence; (c) amplifying the nucleic acid molecules of the target library with incorporated tag adaptors to produce an input library comprising a first plurality of amplified DNA molecules, wherein the amplified molecules comprise sequence identical to or complementary to at least a portion of the first tag adaptor molecule, sequence identical to or complementary to at least a portion of at least one member of the target library, and sequence identical to or complementary to at least a portion of the second tag adaptor molecule; (d) fragmenting the input library to produce a plurality of linear DNA fragments having a first end and a second end; (e) attaching at least one nucleic acid shotgun adaptor molecule to one or both ends of at least one of the plurality of linear DNA fragments, wherein at least a portion of the shotgun adaptor molecule comprises a defined shotgun sequence; and (f) amplifying the plurality of linear DNA fragments to produce a sequencing library comprising a second plurality of amplified DNA molecules, wherein at least one of the plurality of amplified DNA molecules comprises sequence identical to or complementary to at least a portion of the first to adaptor molecule, sequence identical to or complementary to at least a portion of the shotgun adaptor molecule, and sequence identical to or complementary to at least a portion of a member of the target library, and wherein at least one of the plurality of amplified DNA molecules comprises sequence identical to or complementary to at least a portion of the second tag adaptor molecule, sequence identical to or complementary to at least a portion of the shotgun adaptor molecule, and sequence identical to or complementary to at least a portion of a member of the target library. - View Dependent Claims (19, 20, 21, 22, 23, 24, 25, 26, 27, 28)
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Specification