Klebsiella phage infection studied by single-cell level by Atrandi spplit-and-pool barcoding

Split-and-pool barcoding simplifies single-cell omics by constructing unique barcode strings in a 96-well plate format, eliminating the need for costly equipment. CleanBar, a flexible demultiplexing tool, processes reads tagged with sequentially ligated barcodes, compatible with various sequencing methods and platforms. It handles variations in barcode positions, linker lengths, and ligation errors, while providing useful statistics for optimizing lab procedures. Demonstrated with the Atrandi platform and PacBio sequencing, CleanBar overcomes bulk metagenomics limitations in phage-bacteria interaction studies. Single-cell analysis revealed infection heterogeneity and precise phage quantification in an experiment with four different Klebsiella strains and their phages, showcasing potential of CleanBar for high-throughput microbial genomics and advancing ecological and evolutionary research.