crispr-screens

crispr-screens is a containerized Snakemake workflow for the analysis of CRISPR screens. It provides a scalable and highly reproducible analysis pipeline.

Contents

Experimental considerations

• Model system
• sgRNA library selection
• sgRNA library transduction and representation
• Sample comparisons
• References

Installion of required software

• Conda
• Snakemake
• Apptainer
  • Installation on a local machine
  • Installation on HPC systems
• Snakefetch
• Obtaining workflow code

Workflow usage

• Preparing analysis data directory
• Experiment meta data
• FASTQ trimming
• BAGEL2 analysis
• MAGeCK analysis
  • RRA
  • MLE
• drugZ analysis
• CRISPRcleanR
• Setup global Snakemake profile
• Dry-run on experimental data
• Execution of workflow
• Report of analysis

Protocols

• Protocols
• References

About

• About crispr-screens
• Citation

Source code

• Reporting issues