Welcome to Brieflow

Brieflow is tool written with Snakemake that simplifies and automates many of the steps in optical pooled screen (OPS) analysis. Although written to be easily deployed on a Slurm cluster, it can also be run on other cloud-based or local systems. We have built Brieflow in tandem with brieflow-analysis to configure and organize Brieflow runs.

Brieflow currently automates the following OPS tasks:

• Preprocessing: Converts raw microscope .nd2 files into tiled .tiff images and extracts associated metadata (e.g. cycle, tile, well).

• SBS: Identifies and decodes in situ sequencing barcodes from fluorescence imaging data.

• Phenotype: Extracts morphological and intensity-based features for each cell from the imaging data.

• Merge: Matches phenotypic features with decoded barcodes across cycles and imaging rounds.

• Aggregate: Aggregates single-cell data by perturbation or barcode, producing summary-level datasets.

• Cluster: Performs unsupervised clustering to identify patterns or phenotypic signatures across perturbations.

We recommend you view the doc pages below (in order) before using brieflow/brieflow-analysis to ensure you have a good understanding of the system.

Brieflow is a community-driven project, and we welcome contributions from anyone interested in improving the tool :)

Contents:

• 0. Brieflow <> Brieflow Analysis
  • Overview
  • Brieflow
  • Brieflow Analysis
  • Reproducibility and Modularity
• 1. Before You Screen
  • Resources
  • OPS Data Collection
• 2. Installation & Analysis Setup
  • Standard Workflow (Recommended)
  • Developer Workflow
• 3. Running Modules
  • Overview
  • Getting Started
  • Workflow
  • HPC Integrations
  • Module-by-Module Instructions
  • Example Video
  • Additional Notes
• 4. Visualization
  • Overview
  • Getting Started
  • Environment Variables
  • Application Sections
  • Tips
• 5. Development
  • Overview
  • Screen Adaptation
  • Contributing
• Example Analyses
  • Denali Screen
  • Aconcagua Screen
• Config Glossary