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Accurate analysis of genuine CRISPR editing events with ampliCan.

ABSTRACT: 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.

SUBMITTER: Labun K

PROVIDER: S-EPMC6499316 | biostudies-literature | 2019 May

REPOSITORIES: biostudies-literature

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Accurate analysis of genuine CRISPR editing events with ampliCan.

Labun Kornel K Guo Xiaoge X Chavez Alejandro A Church George G Gagnon James A JA Valen Eivind E

Genome research 20190308 5

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 CRIS ...[more]

PMID: 30850374

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