The number of commercially available Unique Dual Index (UDI) primer pairs remains limited, with few commercial offerings above 1,536 UDI pairs. In an era of ever-increasing sequencing capacity, this unnecessarily limits sample throughput and increases the cost per sample. To address these limitations, Twist Bioscience developed a new set of 3,072 UDIs that enables higher sample throughput in large experiments. 

The design of large sets of barcodes can be difficult due to the exponential nature of barcode-barcode interactions. Twist’s design approach includes (i) sophisticated index design, (ii) subsetting index pairs into bins that are base and color channel balanced, and (iii) empirical validation of each index pair across multiple sequencing platforms. This approach enabled the generation of a large and performant set of UDI primers described here.