A multifunctional adaptor comprising: a) a ligation strand oligonucleotide, and b) a non-ligation strand oligonucleotide that is capable of hybridizing to a region at the 3' end of the ligation strand oligonucleotide and forming a duplex therewith; wherein, upon contact with a dsDNA fragment from a sample, the ligation strand oligonucleotide ligates to the 5' end of each strand of the dsDNA fragment; wherein the ligation strand oligonucleotide comprises: i) a 3' terminal overhang; ii) an amplification region comprising a polynucleotide sequence capable of serving as a primer recognition site; iii) a unique multifunctional ID region; iv) a unique molecule identifier multiplier; and v) an anchor region comprising a polynucleotide sequence that is at least partially complementary to the non-ligation strand oligonucleotide; wherein the dsDNA fragment comprises a phosphate group at the 5' terminus of each strand and an overhang at the 3' terminus of each strand; wherein the combination of the multifunctional ID region and the UMI multiplier identifies the dsDNA fragment; and wherein the multifunctional ID region identifies the sample. a) a ligation strand oligonucleotide, and b) a non-ligation strand oligonucleotide that is capable of hybridizing to a region at the 3' end of the ligation strand oligonucleotide and forming a duplex therewith; wherein, upon contact with a dsDNA fragment from a sample, the ligation strand oligonucleotide ligates to the 5' end of each strand of the dsDNA fragment; wherein the ligation strand oligonucleotide comprises: i) a 3' terminal overhang; ii) an amplification region comprising a polynucleotide sequence capable of serving as a primer recognition site; iii) a unique multifunctional ID region; iv) a unique molecule identifier multiplier; and v) an anchor region comprising a polynucleotide sequence that is at least partially complementary to the non-ligation strand oligonucleotide; wherein the dsDNA fragment comprises a phosphate group at the 5' terminus of each strand and an overhang at the 3' terminus of each strand; wherein the combination of the multifunctional ID region and the UMI multiplier identifies the dsDNA fragment; and wherein the multifunctional ID region identifies the sample. wherein, upon contact with a dsDNA fragment from a sample, the ligation strand oligonucleotide ligates to the 5' end of each strand of the dsDNA fragment; wherein the ligation strand oligonucleotide comprises: i) a 3' terminal overhang; ii) an amplification region comprising a polynucleotide sequence capable of serving as a primer recognition site; iii) a unique multifunctional ID region; iv) a unique molecule identifier multiplier; and v) an anchor region comprising a polynucleotide sequence that is at least partially complementary to the non-ligation strand oligonucleotide; i) a 3' terminal overhang; ii) an amplification region comprising a polynucleotide sequence capable of serving as a primer recognition site; iii) a unique multifunctional ID region; iv) a unique molecule identifier multiplier; and v) an anchor region comprising a polynucleotide sequence that is at least partially complementary to the non-ligation strand oligonucleotide; wherein the dsDNA fragment comprises a phosphate group at the 5' terminus of each strand and an overhang at the 3' terminus of each strand; wherein the combination of the multifunctional ID region and the UMI multiplier identifies the dsDNA fragment; and wherein the multifunctional ID region identifies the sample.