Compositions and methods for improving sample identification in indexed nucleic acid libraries

An oligonucleotide adapter for ligating to a target polynucleotide prior to sequencing, comprising:

• a first oligonucleotide strand having a 5′ end and a 3′ end;
• and
• a second oligonucleotide strand having a 5′ end and a 3′ end,
• wherein a region of the 5′ end of the first strand comprises nucleotides complementary to nucleotides in a region of the 3′ end of the second strand such that the complementary regions are double-stranded,
• wherein a region of the 3′ end of the first strand and a region of the 5′ end of the second strand are sufficiently non-complementary to be single-stranded,
• wherein at least one of the first strand and the second strand comprises a library-specific index tag sequence,
• wherein the 3′ end of the first strand is modified to prevent digestion by an enzyme having 3′ exonuclease activity and wherein the 5′ end of the second strand is modified to prevent digestion by an enzyme having 5′ exonuclease activity, and
• wherein the 5′ end of the first strand is susceptible to exonuclease activity and wherein the 3′ end of the second strand is susceptible to exonuclease activity.