CRISPResso

CRISPResso is an open-source software suite for the analysis of genome editing experiments. Developed to provide accurate, reproducible quantification of CRISPR outcomes, CRISPResso has become the most widely cited tool in its class, trusted by researchers and commercial organizations worldwide.

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
  • Support for multiple experiment types 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 alignment algorithms are designed with biology in mind, producing the most accurate quantification of editing outcomes by accounting 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 Tools

The CRISPResso suite includes specialized tools for different analysis needs:

  • CRISPResso2 - Core analysis tool for single amplicon experiments
  • CRISPRessoPooled - Analysis of pooled experiments with multiple amplicons
  • CRISPRessoWGS - Whole genome sequencing analysis
  • CRISPRessoCompare - Statistical comparison between samples
  • CRISPRessoPooledWGSCompare - Combined pooled and WGS comparison
  • CRISPRessoAggregate - Aggregate results across multiple runs

Commercial Licensing

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

  • Self-hosting options for secure, on-premise deployment
  • Enterprise support with dedicated assistance
  • Priority updates and feature requests

Contact licensing@edilytics.com for commercial licensing inquiries.

Resources

Getting Started

Install CRISPResso via pip or conda:

pip install CRISPResso2

or

conda install -c bioconda crispresso2

Visit our documentation for detailed installation instructions and tutorials.