Method for the determination of a target nucleotide sequence in a sample comprising the steps of (a) providing for each target nucleotide sequence a first probe and a second probe, wherein the first probe comprises a first target specific section and a first tag section that is non-complementary to the target nucleotide sequence and that optionally comprises a first primer binding sequence, wherein the first tag section comprise a first recognition sequence for a first restriction endonuclease; wherein the second probe comprises a second target specific section and a second tag section that is non-complementary to the target nucleotide sequence and that comprises an optional second primer binding sequence, wherein second tag section comprises a second recognition sequence for a second restriction endonuclease; (b) allowing the first and second target specific section of the respective first and second probe to hybridize to the target sequence; (c) ligating the first and second probe when the respective target specific sections of the probes are hybridized to essentially adjacent sections on the target sequence to provide ligated probes; (d) optionally amplifying the ligated probes with an optional first and/or an optional second primer to provide amplicons; (e) restricting the ligated probes or amplicons with the first and/or second restriction endonuclease to provide restricted ligated probes or restricted amplicons, ligating a first and/or a second adapter containing an adapter-based identifier (AD ID1, AD ID2) to the restricted ligated probes or restricted amplicons; (f) subjecting the adapter-ligated restricted ligated probes or adapter-ligated restricted amplicons to high throughput sequencing technology to determine at least part of the nucleotide sequence of the restricted ligated probes or restricted amplicons; (g) identifying the presence, absence or amount of the target nucleotide sequence in the sample. (a) providing for each target nucleotide sequence a first probe and a second probe, wherein the first probe comprises a first target specific section and a first tag section that is non-complementary to the target nucleotide sequence and that optionally comprises a first primer binding sequence, wherein the first tag section comprise a first recognition sequence for a first restriction endonuclease; wherein the second probe comprises a second target specific section and a second tag section that is non-complementary to the target nucleotide sequence and that comprises an optional second primer binding sequence, wherein second tag section comprises a second recognition sequence for a second restriction endonuclease; wherein the first probe comprises a first target specific section and a first tag section that is non-complementary to the target nucleotide sequence and that optionally comprises a first primer binding sequence, wherein the first tag section comprise a first recognition sequence for a first restriction endonuclease; wherein the second probe comprises a second target specific section and a second tag section that is non-complementary to the target nucleotide sequence and that comprises an optional second primer binding sequence, wherein second tag section comprises a second recognition sequence for a second restriction endonuclease; (b) allowing the first and second target specific section of the respective first and second probe to hybridize to the target sequence; (c) ligating the first and second probe when the respective target specific sections of the probes are hybridized to essentially adjacent sections on the target sequence to provide ligated probes; (d) optionally amplifying the ligated probes with an optional first and/or an optional second primer to provide amplicons; (e) restricting the ligated probes or amplicons with the first and/or second restriction endonuclease to provide restricted ligated probes or restricted amplicons, ligating a first and/or a second adapter containing an adapter-based identifier (AD ID1, AD ID2) to the restricted ligated probes or restricted amplicons; (f) subjecting the adapter-ligated restricted ligated probes or adapter-ligated restricted amplicons to high throughput sequencing technology to determine at least part of the nucleotide sequence of the restricted ligated probes or restricted amplicons; (g) identifying the presence, absence or amount of the target nucleotide sequence in the sample.