Array-based oligonucleotide synthesis can be used to generate primer pools for use in MPE-seq Steps during the amplification and purification of array-synthesized primer pools are monitored via native gel electrophoresis. The control lane represents a pool of individually synthesized MPE-seq primers which did not require amplification and purification. Lanes refer to products of each individual step in the protocol. (1) PCR amplification of the oligonucleotide synthesis pool using a 5’ blocked sense primer and a biotinylated antisense primer. (2) Restriction digestion to cleave off the PCR primer handle. (3) Lambda exonuclease digestion of free 5’ ends. (4) Streptavidin purification of biotinylated PCR handle. The unbound fraction is the desired primer pool product. 