PT  - JOURNAL ARTICLE
AU  - Labun, Kornel
AU  - Guo, Xiaoge
AU  - Chavez, Alejandro
AU  - Church, George
AU  - Gagnon, James
AU  - Valen, Eivind
TI  - Accurate analysis of genuine CRISPR editing events with ampliCan
AID  - 10.1101/249474
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 249474
4099  - http://biorxiv.org/content/early/2018/09/15/249474.short
4100  - http://biorxiv.org/content/early/2018/09/15/249474.full
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, 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 datasets against other leading tools, demonstrating that it outperformed all in the face of common confounding factors.