A system for target specific templating of a Cas recognition element comprising: a plurality of nucleic acid molecules having different nucleotide sequences; a set of ligation oligonucleotides, comprising: a first ligation oligonucleotide whose nucleotide sequence includes a templating element and a first target hybridization element, wherein the templating element i) is or comprises a promoter or complement thereof; ii) is or comprises an origin of replication or complement thereof; iii) is or comprises a binding site for a first extendable primer; or iv) is or comprises one or more transcriptional regulatory elements; and a second ligation oligonucleotide whose nucleotide sequence includes a second target hybridization element and a Cas recognition element, wherein the Cas recognition element is a nucleotide sequence or complement thereof that is bound by a Cas guide RNA; and a guide RNA capable of binding to said Cas recognition element, optionally one or more bridging oligonucleotides whose nucleotide sequence is or comprises one or more additional target hybridization elements, wherein the target hybridization elements bind to different portions of a common target site, so that, when the plurality of nucleic acid molecules includes at least one target nucleic acid molecule whose nucleotide sequence includes the target site, then the set of ligation oligonucleotides hybridizes to the target site and forms a gapped nucleic acid strand susceptible to ligation with a ligase to generate a ligated strand. a plurality of nucleic acid molecules having different nucleotide sequences; a set of ligation oligonucleotides, comprising: a first ligation oligonucleotide whose nucleotide sequence includes a templating element and a first target hybridization element, wherein the templating element i) is or comprises a promoter or complement thereof; ii) is or comprises an origin of replication or complement thereof; iii) is or comprises a binding site for a first extendable primer; or iv) is or comprises one or more transcriptional regulatory elements; and a second ligation oligonucleotide whose nucleotide sequence includes a second target hybridization element and a Cas recognition element, wherein the Cas recognition element is a nucleotide sequence or complement thereof that is bound by a Cas guide RNA; and a first ligation oligonucleotide whose nucleotide sequence includes a templating element and a first target hybridization element, wherein the templating element i) is or comprises a promoter or complement thereof; ii) is or comprises an origin of replication or complement thereof; iii) is or comprises a binding site for a first extendable primer; or iv) is or comprises one or more transcriptional regulatory elements; and a second ligation oligonucleotide whose nucleotide sequence includes a second target hybridization element and a Cas recognition element, wherein the Cas recognition element is a nucleotide sequence or complement thereof that is bound by a Cas guide RNA; and a guide RNA capable of binding to said Cas recognition element, optionally one or more bridging oligonucleotides whose nucleotide sequence is or comprises one or more additional target hybridization elements, wherein the target hybridization elements bind to different portions of a common target site, so that, when the plurality of nucleic acid molecules includes at least one target nucleic acid molecule whose nucleotide sequence includes the target site, then the set of ligation oligonucleotides hybridizes to the target site and forms a gapped nucleic acid strand susceptible to ligation with a ligase to generate a ligated strand.