Quantifying orthogonal barcodes for sequence census assays

Abstract Summary Barcode-based sequence census assays utilize custom or random oligonucloetide sequences to label various biological features, such as cell-surface proteins or CRISPR perturbations. These assays all rely on barcode quantification, a task that is complicated by barcode design and technical noise. We introduce a modular approach to quantifying barcodes that achieves speed and memory improvements over existing tools. We also introduce a set of quality control metrics, and accompanying tool, for validating barcode designs. Availability and implementation https://github.com/pachterlab/kb_python, https://github.com/pachterlab/qcbc.