pinellolab/crispresso2 repository overview

⁠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.