CRISPResso2

CRISPResso2 is a software pipeline designed to enable rapid and intuitive interpretation of genome editing experiments. A limited web implementation is available at: https://crispresso2.pinellolab.org/.

Briefly, CRISPResso2:

• aligns sequencing reads to a reference sequence
• quantifies insertions, mutations and deletions to determine whether a read is modified or unmodified by genome editing
• summarizes editing results in intuitive plots and datasets

Access the full documentation at https://docs.crispresso.com.

In addition, CRISPResso can be run as part of a larger tool suite:

• CRISPRessoBatch - for analyzing and comparing multiple experimental conditions at the same site
• CRISPRessoPooled - for analyzing multiple amplicons from a pooled amplicon sequencing experiment
• CRISPRessoWGS - for analyzing specific sites in whole-genome sequencing samples
• CRISPRessoCompare - for comparing editing between two samples (e.g., treated vs control)
• CRISPRessoAggregate - for aggregating results from previously-run CRISPResso analyses

Installation

CRISPResso2 can be installed in the following ways:

• Bioconda
  • Bioconda on Apple Silicon
• Docker

Examples

• CRISPResso example runs
• CRISPRessoBatch example runs
• CRISPRessoPooled example runs
• CRISPRessoWGS example runs
• CRISPRessoCompare example runs
• CRISPRessoPooledWGCompare example runs
• CRISPRessoAggregate example runs

Troubleshooting

If you run into any issues, check out the Troubleshooting page or submit a new discussion.