bio-crispr-screens-crispresso-editing

name	bio-crispr-screens-crispresso-editing
description	CRISPResso2 for analyzing CRISPR gene editing outcomes. Quantifies indels, HDR efficiency, and generates comprehensive editing reports. Use when analyzing amplicon sequencing data from CRISPR editing experiments to assess editing efficiency.
tool_type	cli
primary_tool	CRISPResso2

Version Compatibility

Reference examples tested with: CRISPResso2 2.2+, pandas 2.2+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures
• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

CRISPResso2 Editing Analysis

"Quantify CRISPR editing from my amplicon data" → Analyze amplicon sequencing to measure indel frequencies, HDR efficiency, and frameshift rates from CRISPR gene editing experiments.

• CLI: CRISPResso --fastq_r1 reads.fq --amplicon_seq ATGC --guide_seq GUIDE

Basic Analysis

Goal: Quantify CRISPR editing outcomes from amplicon sequencing of a single target site.

Approach: Align amplicon reads against the reference and guide sequences with CRISPResso, which reports indel frequencies, allele tables, and editing efficiency plots.