RT Journal
A1 Labun, Kornel
A1 Guo, Xiaoge
A1 Chavez, Alejandro
A1 Church, George
A1 Gagnon, James A.
A1 Valen, Eivind
T1 Accurate analysis of genuine CRISPR editing events with ampliCan
JF Genome Research 
JO Genome Research 
YR 2019 
FD May 01 
VO 29 
IS 5 
SP 843 
OP 847 
DO 10.1101/gr.244293.118 
UL http://genome.cshlp.org/content/29/5/843.abstract 
AB 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.