A method for targeted enrichment of nucleic acids, the method comprising: contacting a nucleic acid including at least one region of interest with a plurality of transposase complexes, each of the transposase complexes including at least a transposase and a first polynucleotide, the first polynucleotide having a transposon end sequence and a first label sequence, the transposon end sequence corresponding to the first transposase; incubating the nucleic acid and the transposase complexes under conditions whereby multiple transposon end sequences and associated label sequences are inserted into the nucleic acid and the nucleic acid is fragmented into a plurality of nucleic acid fragments including first polynucleotide attached to each 5' end of the nucleic acid fragments; selectively amplifying the nucleic acid fragments, thereby enriching for a portion of the nucleic acid fragments including the at least one region of interest relative to a remaining portion of the nucleic acid fragments; and sequencing the enriched nucleic acid fragments. wherein selectively amplifying the nucleic acid fragments further includes a first round of PCR with at least one region specific primer complementary to the nucleic acid proximal to the at least one region of interest, and a label specific primer complementary to at least a portion of the first label sequence attached to each 5' end of the nucleic acid fragments, wherein selectively amplifying the nucleic acid fragments further includes at least ten region specific primers, wherein each of the region specific primers are complementary to the nucleic acid proximal to different regions of interest. contacting a nucleic acid including at least one region of interest with a plurality of transposase complexes, each of the transposase complexes including at least a transposase and a first polynucleotide, the first polynucleotide having a transposon end sequence and a first label sequence, the transposon end sequence corresponding to the first transposase; incubating the nucleic acid and the transposase complexes under conditions whereby multiple transposon end sequences and associated label sequences are inserted into the nucleic acid and the nucleic acid is fragmented into a plurality of nucleic acid fragments including first polynucleotide attached to each 5' end of the nucleic acid fragments; selectively amplifying the nucleic acid fragments, thereby enriching for a portion of the nucleic acid fragments including the at least one region of interest relative to a remaining portion of the nucleic acid fragments; and sequencing the enriched nucleic acid fragments. wherein selectively amplifying the nucleic acid fragments further includes a first round of PCR with at least one region specific primer complementary to the nucleic acid proximal to the at least one region of interest, and a label specific primer complementary to at least a portion of the first label sequence attached to each 5' end of the nucleic acid fragments, wherein selectively amplifying the nucleic acid fragments further includes at least ten region specific primers, wherein each of the region specific primers are complementary to the nucleic acid proximal to different regions of interest.