CRISPResso

CRISPResso is the standard genome editing quantification tool. It is widely used in academic and industry labs and has become the most widely cited tool in its class. CRISPResso produces reliable and easy to interpret results so you can know exactly what is happening in your experiment.

What is CRISPResso?

CRISPResso analyzes next-generation sequencing (NGS) data from CRISPR genome editing experiments to quantify editing outcomes. It provides:

  • Accurate quantification of insertions, deletions, and substitutions
  • Standardized visualizations recognized across the field
  • Full data access to perform your own downstream analysis
  • Rich customization for analyzing any nuclease
  • Support for multiple experiment modalities including base editing, prime editing, and HDR

Key Features

Open Source

CRISPResso is freely available for research and academic use under an open-source license. The source code is publicly available on GitHub, enabling transparency and community contributions.

Biologically Informed Alignment

Our novel alignment algorithm produces the most accurate alignments for genome editing data. The alignment is developed to account for the specific characteristics of CRISPR-induced modifications.

Easy to Use

Available as both a command-line interface for high-throughput analysis and a web interface for accessibility. Comprehensive documentation helps you get started quickly.

Complete Data Access

Every plot and visualization is backed by accessible raw data, allowing you to perform custom downstream analysis and integrate results into your workflows.

Comprehensive Visualizations

Generate publication-ready figures that clearly communicate your editing outcomes, including allele plots, indel size distributions, and nucleotide frequency charts.

CRISPResso Suite

The CRISPResso suite includes specialized tools for different analysis needs:

  • CRISPResso - Core analysis tool for single amplicon experiments
  • CRISPRessoPooled - Analysis of pooled experiments with multiple amplicons
  • CRISPRessoWGS - Whole genome sequencing analysis of targeted regions
  • CRISPRessoCompare - Statistical comparison between CRISPResso analyses
  • CRISPRessoAggregate - Aggregate results across multiple runs

Commercial Licensing

While CRISPResso is open source for academic use, commercial use requires a license from Edilytics. Commercial licensing includes:

  • Self-hosting options for secure, on-premise deployment of the CLI and web interface
  • Enterprise support with dedicated assistance

Contact licensing@edilytics.com for commercial licensing inquiries, or visit the Contact page.

Resources

Getting Started

Visit crispresso.com to run your analysis.

Or install CRISPResso locally via conda:

conda install -c bioconda crispresso2

Visit our installation documentation for other installation options, more detailed instructions and tutorials.