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ViroConstrictor Architecture

ViroConstrictor is a Snakemake-based bioinformatics pipeline designed for viral genome consensus sequence generation from NGS data. The architecture follows a modular design with distinct workflows for different analysis scenarios.

Overview

ViroConstrictor consists of two main workflows: 1. Main Workflow: Standard viral genome analysis pipeline 2. Match-Reference Workflow: Multi-reference selection and analysis

The pipeline is built using Snakemake, providing scalability, reproducibility, and flexible execution across different computing environments.

Architecture Components

Core Structure

ViroConstrictor/
├── workflow/
│   ├── main/                    # Primary analysis workflow
│   │   ├── workflow.smk         # Main workflow entry point
│   │   └── components/          # Modular rule components
│   ├── match_ref/               # Reference selection workflow
│   │   ├── workflow.smk         # Match-ref workflow entry point
│   │   └── components/          # Match-ref specific components
│   ├── helpers/                 # Shared utility functions
│   └── envs/                    # Conda environment definitions
├── scheduler.py                 # Grid system auto-detection
├── workflow_executor.py         # Execution orchestration
└── ...

Workflow Components

The main workflow is organized into logical processing stages:

1. Preparation Stage

  • Reference Processing (preparation.references.smk)
  • Primer Processing (preparation.primers.smk)
  • Feature Processing (preparation.features.smk)

2. Quality Control & Cleaning

  • Pre-cleaning Stats (stats.pre_clean.smk)
  • Adapter Removal (clean.adapter_removal.smk)
  • Data Filtering (clean.data_filter.smk)
  • Primer Removal (clean.primer_removal.smk)
  • Post-cleaning Stats (stats.post_clean.smk)

3. Results Generation

  • Sequence Generation (results.sequences.smk)
  • Reporting Metrics (results.reporting_metrics.smk)
  • Data Concatenation (results.concatenations.smk)

Workflow Execution Flow

Standard Analysis Flow

graph TD
    A[Input FASTQ Files] --> B[Pre-cleaning QC]
    A --> C[Adapter Removal]
    C --> D[Data Filtering]
    D --> E[Primer Removal]
    E --> F[Post-cleaning QC]
    E --> G[Reference Alignment]
    G --> H[Consensus Calling]
    H --> I[Feature Extraction]
    I --> J[Report Generation]
    J --> K[Final Results]
    B --> J
    F --> J

Match-Reference Flow

graph TD
    A[Input FASTQ Files] --> B[Reference Preparation]
    B --> C[Initial Alignment]
    C --> D[Reference Selection]
    D --> E[Standard Analysis Flow]
    E --> F[Results per Reference]