bio-workflows-crispr-screen-pipeline

What problem does it solve?

Automates the end-to-end analysis of pooled CRISPR screens, from raw FASTQ data through guide counting, QC, MAGeCK statistical testing, and hit calling, enabling researchers to identify candidate genes efficiently.

Core Features & Use Cases

• End-to-end pipeline: from FASTQ to hit lists with multiple methods (MAGeCK, BAGEL2).
• QC and replicate assessment to ensure robust results.
• Flexible designs: supports single or multi-condition experiments, including CRISPRi/CRISPRa, dropout and enrichment screens.
• Generates plots and reports for easy interpretation.

Quick Start

Run the CRISPR screen pipeline on your pooled screen FASTQ data to generate guide counts, QC metrics, hit calls, and visualization outputs.