What problem does it solve? Quantifying CRISPR editing outcomes from amplicon sequencing requires choosing the correct CRISPResso2 mode, sizing the quantification window correctly, and distinguishing intended edits from bystander edits, indel byproducts, and contamination—mistakes in any of these silently corrupt reported editing efficiencies. ## Core Features & Use Cases - Mode selection and execution: Covers CRISPResso (single amplicon), CRISPRessoBatch (multi-sample), CRISPRessoPooled (multi-amplicon pools), CRISPRessoWGS (off-target from BAM), and CRISPRessoCompare (pairwise comparison), with a decision tree mapping experimental design to mode. - Editor-specific quantification: Handles Cas9 nuclease (indels, HDR), cytosine and adenine base editors (target conversion plus bystander rates, substitution-vs-indel diagnostic), and prime editors (intended edit vs scaffold incorporation vs indels). - Failure diagnosis: Documents low-alignment causes, the silent --min_reads_to_use_region default that yields all-NA pooled results, MMEJ deletion signatures in allele tables, and quantitative thresholds for KO efficiency, BE purity, and PE quality. - Use Case: A researcher with a 24-sample Cas9 timecourse runs CRISPRessoBatch, verifies mapping rate above 85%, parses the aggregated quantification table in pandas, and flags samples below the 70% indel threshold for incomplete knockout. ## Quick Start Ask the agent to quantify the indel rate at your Cas9 cut site from paired-end amplicon FASTQ files using your primer-trimmed amplicon sequence and 20-nt guide, and to report unmodified versus NHEJ percentages with the retained-read fraction.
