ENCODED ASSAYS

1 . A method of conducting an assay for a set of targets, the method comprising:

(a) providing a sample comprising a set of targets;

(b) subjecting the sample to a recognition event, in which one or more targets in the set of targets in the sample is hybridized to a recognition element comprising a code from a set of codes, thereby yielding a set of coded targets comprising one or more targets and the recognition element;

(c) subjecting each recognition element of the set of coded targets to a transformation event, in which a molecular transformation of each recognition element of the set of coded targets produces a circular recognition element, thereby yielding a set of circular recognition elements comprising the code;

(d) subjecting each circular recognition element to a rolling circle amplification event to produce a set of amplified codes; and

(e) subjecting each amplified code of the set of amplified codes to a detection event, wherein the detection event determines the presence of the coded targets.

2 . The method of claim 1 , further comprising subjecting the amplified codes to an exonuclease cleanup step.

3 . The method of claim 1 , further comprising:

(f) counting codes of an amplified code of the set of amplified codes that has been subjected to the detection event; and

(g) estimating a quantity of the target based on the codes that are counted in (f).

4 . (canceled)

5 . The method of claim 1 , wherein each code from the set of codes has a length of 3 to 75 nucleotides.

6 - 8 . (canceled)

9 . The method of claim 1 , wherein each code from the set of codes is homopolymer free.

10 . The method of claim 1 , wherein each code from the set of codes is generated from a 4-ary nucleotide alphabet of adenosine (A), cytosine (C), guanine (G) and thymine (T).

11 . (canceled)

12 . The method of claim 1 , wherein each code from the set of codes is generated from a 3-ary nucleotide alphabet comprising A, C, G and T.

13 . The method of claim 1 , wherein the code is generated using a 4-state encoding trellis with 3 transitions per state.

14 . The method of claim 1 , wherein the recognition element comprises one or more universal primers associated with the code.

15 - 22 . (canceled)

23 . The method of claim 1 , wherein the transformation event comprises ligating termini of the recognition element together in the presence of the target but not in the absence of the target.

24 - 37 . (canceled)

38 . The method of claim 1 , wherein the target of the set of targets comprises one or more mutated nucleic acid sequences.

39 . The method of claim 1 , wherein the target of the set of targets comprises one or more point mutations.

40 . The method of claim 1 , wherein the target of the set of targets comprises one or more substitutions, insertions and/or deletions.

41 . The method of claim 1 , wherein the target of the set of targets comprises one or more copy number variations.

42 - 155 . (canceled)

156 . The method of claim 1 , wherein the target of the set of targets is a methylated nucleic acid sequence.

157 . The method of claim 1 , wherein the detection event comprises obtaining a fluorescence measurement.

158 . The method of claim 1 , wherein the set of coded targets further comprises one or more sequencing adapters for sequencing, and wherein the method is a multiplexed method further comprising performing sequencing.

159 . The method of claim 1 , further comprising immobilizing the amplified codes on a surface, wherein the detection event comprises imaging the amplified codes immobilized on the surface with a fluorescence optical measurement system.

160 . The method of claim 1 , wherein the method is performed in wells of an assay substrate comprising the wells.

161 . The method of claim 1 , wherein the set of targets comprises 100 targets, and wherein the subjecting in (e) determines a presence of 100 codes of the set of codes in a multiplexed method.