Next-Generation Barcoding for Single-Cell Omics

The ability to uniquely label and track individual cells at scale has become foundational to single-cell omics. Conventional barcoding strategies, ranging from plate-based combinatorial indexing to droplet microfluidics-based indexing, have enabled the rise of high-throughput single-cell profiling. However, these approaches each face trade-offs in throughput, cost, compatibility with complex biochemical workflows, or accessibility to nonspecialist laboratories. This perspective surveys the principles, benefits, and limitations of current barcoding methods and introduces emerging enzymatic and computational methods that may redefine how we uniquely index the cellular content, opening the door to simpler, more scalable, and more accessible single-cell analysis pipelines.