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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.
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Details
1 Division of Biology and Biological Engineering, California Institute of Technology , Pasadena, CA 91125, United States
2 Department of Computer Science and Electrical Engineering, Massachusetts Institute of Technology , Cambridge, MA 02139, United States
3 Arcadia Science , Berkeley, CA 94702, United States