Accurate analysis of genuine CRISPR editing events with ampliCan
Peer reviewed, Journal article
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Original versionLabun K, Guo, Chavez, Church GM, Gagnon JA, Valen E. Accurate analysis of genuine CRISPR editing events with ampliCan. Genome Research. 2019;29(5):843-847 https://doi.org/10.1101/gr.244293.118
We present ampliCan, an analysis tool for genome editing that unites highly precise quantification and visualization of genuine genome editing events. ampliCan features nuclease-optimized alignments, filtering of experimental artifacts, event-specific normalization, and off-target read detection and quantifies insertions, deletions, HDR repair, as well as targeted base editing. It is scalable to thousands of amplicon sequencing–based experiments from any genome editing experiment, including CRISPR. It enables automated integration of controls and accounts for biases at every step of the analysis. We benchmarked ampliCan on both real and simulated data sets against other leading tools, demonstrating that it outperformed all in the face of common confounding factors.