Abstract: Provided herein, inter alia, are methods and compositions for assembling oligonucleotide fragments in vivo. The methods bypass inefficient cloning methods and the requirement for expensive enzymes. The methods may further be used to assemble long fragments of DNA. The methods may be used to generate variant libraries and combinatorial libraries and may be used to trace biological processes. Also provided herein, inter alia, are methods for in vivo DNA barcoding of oligonucleotide sequences. Methods provided herein are contemplated to produce unique barcode-oligonucleotide fusion sequences for identifying and isolating the oligonucleotide sequences, e.g., from a mixture. Accordingly, also provided are methods of identifying an oligonucleotide from a mixture of oligonucleotides.

Abstract: The present disclosure provides methods and compositions that enable the rapid insertion of two or more combinations of genetic elements into a target cell genome, as a single copy and at a defined location. Each specific combination of genetic elements can be characterized within a single cell or in a pooled population via short-read sequencing. This technology allows extremely large combinatorial libraries of small or large DNA sequences to be rapidly constructed and screened as pools repeatedly across perturbations.