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crispresso-editing

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Quantifies CRISPR editing outcomes with CRISPResso2 (Clement 2019 Nat Biotechnol) across Cas9-nuclease (indels, HDR), CBE and ABE base editors (target conversion + bystander), and prime editor (pegRNA-templated) modes. Covers single-amplicon (CRISPResso), multi-sample batch (CRISPRessoBatch), pooled-amplicon (CRISPRessoPooled), WGS off-target (CRISPRessoWGS), and sample-comparison (CRISPRessoCompare) workflows; quantification-window math that controls what is called edited; substitution-vs-indel diagnostic to distinguish BE from Cas9 contamination; MMEJ deletion pattern interpretation; allele-frequency tables; and failure modes from amplicon misalignment or contamination. Use when quantifying editing from amplicon sequencing, choosing CRISPResso mode by design, distinguishing intended edits from bystanders and indel byproducts, debugging low-alignment runs, or generating publication-grade editing reports.

When to use

• Quantifying editing from amplicon sequencing
• Choosing CRISPResso mode by design
• Distinguishing intended edits from bystanders and indel byproducts
• Debugging low-alignment runs
• Generating publication-grade editing reports
• Quantifying indel frequencies and HDR efficiency
• Base editor target conversion and bystander analysis
• Prime editor pegRNA-templated edit quantification

When not to use

• Pooled-amplicon mode applied to amplicons that share primer sequences
• Base editor mode without specifying conversion nucleotides
• Prime editor mode without pegRNA extension sequence

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