Circula: an all-in-one command-line toolkit for cell-free DNA analysis

Circula is a command-line toolkit for cell-free DNA analysis. It is designed to be a one-stop solution for processing cell-free DNA data from raw FASTQ files to machine learning model for disease detection/prediction. Circula is built on top of popular or customized bioinformatics tools such as BWA, trim_galore, and MESA. It is designed to be easy to use, with a simple command-line interface that allows users to run the entire analysis pipeline with a single command, or run customized analysis with ease.

Installation

To use Circula, first install it using pip or conda:

$ pip install circula

OR

$ conda install -c conda-forge circula

Check out the QuickStart section for further information, including how to Installation the project.

Note

This project is under active development.

Contents

• About Circula
• QuickStart
  • Installation
  • Initial setup
  • All-in-one analysis example
  • Power analysis example
• Process
  • Initial setup
  • Single-step process
    • 1. Adapter trimmming (Trim Galore)
    • 2. Genome alignment (bwa-meth)
    • 3. Duplicate removal/marking (Picard)
    • 4. Methyltion extraction (MethylDackel)
    • 5. Nucleosome occupancy calculation (DANPOS2)
    • 6. Window protection score calculation
  • All-in-one process: from FASTQ file to epigenetic modalities calling
  • Resume from a specific step
• QC
  • Methylation distribution
  • Fragment length distribution
  • Dinucleotide frequency
• Power analysis
• Multimodal Epigenetic Sequence Analysis (MESA)
  • Modality perforamce evaluation
  • MESA cross-validation
  • MESA construction
• Basic analysis
  • Principal component analysis (PCA)
  • Differential analysis
  • Clustered heatmap
• API
  • circula