A probe system comprising: (a) a population of nucleic acid molecules that have an extendible 5' or 3' end; (b) a set of barcoded particles that each have a nucleotide sequence comprising: (i) a binding sequence that is complementary to the extendible 3' or 5' end of the nucleic acid molecules of (a), (ii) a unique particle identifier sequence, and (iii) a first template sequence; and (c) a ligation splint comprising a first oligonucleotide and a second oligonucleotide, wherein the first oligonucleotide comprises a first sequence and the first template sequence; and the second oligonucleotide comprises a second sequence that is complementary to the first sequence, and the first template sequence, whereby the first oligonucleotide and the second oligonucleotide hybridize with one another via the respective first and second sequences, wherein where the population of nucleic acid molecules has an extendible 3' end, the first template sequence of the ligation splint is downstream of the first and second sequences of the first and second oligonucleotides, and where the population of nucleic acid molecules has an extendible 5' end, the first template sequence of the ligation splint is upstream of the first and second sequences of the first and second oligonucleotides. (a) a population of nucleic acid molecules that have an extendible 5' or 3' end; (b) a set of barcoded particles that each have a nucleotide sequence comprising: (i) a binding sequence that is complementary to the extendible 3' or 5' end of the nucleic acid molecules of (a), (ii) a unique particle identifier sequence, and (iii) a first template sequence; and (i) a binding sequence that is complementary to the extendible 3' or 5' end of the nucleic acid molecules of (a), (ii) a unique particle identifier sequence, and (iii) a first template sequence; and (c) a ligation splint comprising a first oligonucleotide and a second oligonucleotide, wherein the first oligonucleotide comprises a first sequence and the first template sequence; and the second oligonucleotide comprises a second sequence that is complementary to the first sequence, and the first template sequence, whereby the first oligonucleotide and the second oligonucleotide hybridize with one another via the respective first and second sequences, wherein where the population of nucleic acid molecules has an extendible 3' end, the first template sequence of the ligation splint is downstream of the first and second sequences of the first and second oligonucleotides, and where the population of nucleic acid molecules has an extendible 5' end, the first template sequence of the ligation splint is upstream of the first and second sequences of the first and second oligonucleotides. the first oligonucleotide comprises a first sequence and the first template sequence; and the second oligonucleotide comprises a second sequence that is complementary to the first sequence, and the first template sequence, whereby the first oligonucleotide and the second oligonucleotide hybridize with one another via the respective first and second sequences, wherein where the population of nucleic acid molecules has an extendible 3' end, the first template sequence of the ligation splint is downstream of the first and second sequences of the first and second oligonucleotides, and where the population of nucleic acid molecules has an extendible 5' end, the first template sequence of the ligation splint is upstream of the first and second sequences of the first and second oligonucleotides. <EOS>