Quantifying orthogonal barcodes for sequence census assays

Orthogonal barcodes encode biological and technical information across multimodal, multiplexing, and perturbation assays. Barcode quantification is complicated by design and technical noise, while assay-specific tools can be slow, memory-intensive, and introduce batch effects. kITE quantifies diverse barcode assays with high agreement and lower runtime and memory than comparators, while qcbc detects shared subsequences responsible for improper quantification.