A method, comprising: providing a first library comprising a first plurality of polynucleotides having a first adapter-target-first adapter sequence, wherein the polynucleotides of the first plurality of polynucleotides are double stranded in a region comprising the target and at least a portion of the first adapter on both ends of the target; providing a first primer oligonucleotide configured to hybridize with a portion of the first adapter in proximity to a 3' end of a strand of the first adapter, wherein the 5' end of the first primer oligonucleotide is modified to prevent digestion by an enzyme having 5' exonuclease activity; providing a second primer oligonucleotide configured to hybridize with a complement of a portion of the first adapter in proximity to a 3' end of a strand of the complement of the first adapter, wherein the 5' end of the second primer oligonucleotide is modified to prevent digestion by an enzyme having 5' exonuclease activity; incubating the first library with the first and second primer oligonucleotides in a solution under conditions suitable to amplify the polynucleotides having a first adapter-target-first adapter sequence to produce an amplified first library of polynucleotides having 5' ends modified to prevent digestion by an enzyme having 5' exonuclease activity, wherein the amplified polynucleotides have an amplified first adapter-target-amplified first adapter sequence, and wherein the amplified first adapter sequence comprises a first library-specific sequence; modifying 3' ends of the amplified first library polynucleotides to prevent one or both of (i) digestion by an enzyme having 3' exonuclease activity, or (ii) addition of nucleotides to the 3' end by an enzyme having polymerase activity, thereby generating a protected first library of polynucleotides having modified 5' and 3' ends. providing a first library comprising a first plurality of polynucleotides having a first adapter-target-first adapter sequence, wherein the polynucleotides of the first plurality of polynucleotides are double stranded in a region comprising the target and at least a portion of the first adapter on both ends of the target; providing a first primer oligonucleotide configured to hybridize with a portion of the first adapter in proximity to a 3' end of a strand of the first adapter, wherein the 5' end of the first primer oligonucleotide is modified to prevent digestion by an enzyme having 5' exonuclease activity; providing a second primer oligonucleotide configured to hybridize with a complement of a portion of the first adapter in proximity to a 3' end of a strand of the complement of the first adapter, wherein the 5' end of the second primer oligonucleotide is modified to prevent digestion by an enzyme having 5' exonuclease activity; incubating the first library with the first and second primer oligonucleotides in a solution under conditions suitable to amplify the polynucleotides having a first adapter-target-first adapter sequence to produce an amplified first library of polynucleotides having 5' ends modified to prevent digestion by an enzyme having 5' exonuclease activity, wherein the amplified polynucleotides have an amplified first adapter-target-amplified first adapter sequence, and wherein the amplified first adapter sequence comprises a first library-specific sequence; modifying 3' ends of the amplified first library polynucleotides to prevent one or both of (i) digestion by an enzyme having 3' exonuclease activity, or (ii) addition of nucleotides to the 3' end by an enzyme having polymerase activity, thereby generating a protected first library of polynucleotides having modified 5' and 3' ends.