Error detection in sequence tag directed subassemblies of short sequencing reads

A method for detecting an error occurring in the preparation and/or sequencing of a DNA sequencing library, the method 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 the first adaptor molecule comprises a first defined tag 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 a sequence identical to or complementary to the first defined tag sequence and sequence identical to or complementary to at least a portion of the at least one member of the target library;
• (c) sequencing at least a portion of the plurality of amplified DNA molecules to produce a plurality of sequencing reads corresponding to the at least one member of the target library and comprising a sequence identical to or complementary to the first defined tag sequence;
• (d) grouping the plurality of sequencing reads that correspond to the same at least one member of the target library based solely on the commonality of having the first defined tag sequence or a complement thereof;
• and
• (e) detecting whether an error exists at a nucleotide position, wherein an error exists when variation of nucleotide identity exists among the grouped sequencing reads at a position corresponding to a nucleotide in the at least one member of the target library.

A method for correcting an error occurring in the preparation and/or sequencing of a DNA sequencing library, the method 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 the first adaptor molecule comprises a first defined tag 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 a sequence identical to or complementary to the first defined tag sequence and a sequence identical to or complementary to at least a portion of the at least one member of the target library;
• (c) sequencing at least a portion of the plurality of amplified DNA molecules to produce a plurality of sequencing reads corresponding to the at least one member of the target library and comprising a sequence identical to or complementary to the first defined tag sequence;
• (d) grouping the plurality of sequencing reads that correspond to the at least one member of the target library based solely on the commonality of having the first defined tag sequence or a complement thereof;
• (e) detecting whether an error exists at a nucleotide position, wherein an error exists when variation of nucleotide identity exists among the grouped sequencing reads at a position corresponding to a nucleotide in the at least one member of the target library;
• and
• (f) determining the correct identity of the nucleotide at the position where variation of nucleotide identity is detected, wherein the correct identity is determined based on the consensus of the individual base calls in the plurality of grouped sequencing reads.

A method of detecting an error occurring in the preparation and/or sequencing of a DNA sequencing library, the method comprising:

• (a) grouping a plurality of nucleic acid sequencing reads based solely on the commonality of having a first defined non-degenerate sequence tag, wherein the nucleic acid sequencing reads are produced by:
• (i) 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 the first adaptor molecule comprises the first defined tag sequence;
• (ii) 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 a sequence identical to or complementary to the first defined tag sequence and a sequence identical to or complementary to at least a portion of the at least one member of the target library;
• and
• (iii) sequencing at least a portion of the plurality of amplified DNA molecules to produce the plurality of sequencing reads that each comprise a sequence identical to or complementary to at least a portion of the at least one member of the target library and a sequence identical to or complementary to the first defined tag sequence;
• and
• (b) detecting whether an error exists at a nucleotide position, wherein an error exists when variation of nucleotide identity exists among the grouped sequencing reads at a position corresponding to a nucleotide in the at least one member of the target library.