(a) Parallel synthesis of custom oligonucleotides. Constructed sequences are cleaved from the substrate forming a mixed pool of >104 kinds of oligonucleotides with a certain frequency of errors (red). (b) NGS-based massively parallel identification was followed by clone bead location targeting using a diffusion-like local mapping algorithm. NGS enables the isolation and amplification of single molecules from a complex pool to supply a huge amount of sequencing data (105) with accordant pixel information. Our diffusion-like local mapping algorithm overcomes the random and non-linear distortion of the sequencer’s imaging system and converts the pixel information into a real-world location of the target clone bead. (c) Sniper retrieval of target clone beads. Precise location data from the clone bead targeting step and non-contact pulse laser bead retrieval system enable high-throughput (two beads per second) selective separation of 104 perfect regions without cross-contamination. The integrated process of parallel synthesis (DNA microarray), parallel identification (NGS) and high-throughput separation (pulse laser optical retrieval system) dramatically reduces the necessary resources by eliminating the randomness of the conventional cloning method; this provides a huge amount of ultra-high quality artificial oligonucleotides within several days.