KIDS25-Team4 WGS–MTE Pipeline Project

This repository tracks the development of a computational biology pipeline consisting of two major modules:

• Whole-Genome Sequencing (WGS)
• MitoEdit (MTE)

The goal is to:

1. Build and modernize the pipeline for usability and reproducibility.
2. Add functionality, containerization, and visualization features.
3. Provide a clear record of progress, priorities, and ownership.

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📋 Project Task List

Team members can check off items as they are completed.
Use GitHub Projects for detailed tracking, assignments, and prioritization.

WGS

• User Interface: develop UI and capture parameters (BAM list, project name, output path).
• Containerization: package Conda environment and build Docker/Singularity container.
• Validation: compare Nextflow outputs vs HOX8 legacy pipeline.
• Data Prep: create down-sampled BAMs (800M, 500M, 200M reads) for Biohackathon.

MTE Functionality Improvements

• Report whether TALEs are not ideal (not just ideal ones).
• Extend customization module to predict bystander edits.
• Improve parsing to reduce argument failures.

MTE TALEN-NT Modernization

• Rewrite in Python 3.
• Make importable as a library (not only CLI).
• Remove absolute paths.
• Add parallelization for speed.

Visualization

• Add interactive visualization (IGV-like).
  Options:
  • Use Jandee’s agent
  • JavaScript-based implementation

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🗂 Clarified Outline

WGS Module

1. User Interface
   • Define required inputs:
     • Paired BAM list (sample sheet)
     • Project name
     • Output location
   • Build UI to capture these parameters.
2. Dependencies & Containerization
   • Current HPC modules:
     • samtools/1.12, bwa/0.7.17, annovar/20200607, python/3.11.0, bambino-1.0.jar
   • Package into Conda and containerize with Docker/Singularity.
3. Validation
   • Benchmark Nextflow outputs against HOX8 pipeline results.
   • Provide down-sampled BAM files for testing/development.

MTE Module

1. Functionality Improvements
   • Flag non-ideal TALEs.
   • Predict impact of bystander edits.
   • Improve argument parsing robustness.
2. TALEN-NT Modernization
   • Port from Python 2 → Python 3.
   • Implement as importable library.
   • Remove hardcoded paths.
   • Add parallelization.

Visualization

• Add IGV-like interactive viewer for results.
• Options: Jandee’s agent or JavaScript implementation.

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📊 Workflow Diagram

flowchart TD
    A[WGS Module] --> B1[User Interface]
    B1 --> B2[Define input parameters: BAM list, project name, output]
    A --> C1[Dependencies & Containerization]
    C1 --> C2[Package Conda environment]
    C2 --> C3[Build Docker/Singularity container]
    A --> D1[Validation]
    D1 --> D2[Compare outputs with HOX8 pipeline]
    D1 --> D3[Use down-sampled BAM files]

    E[MitoEdit Module] --> F1[Functionality Improvements]
    F1 --> F2[Report non-ideal TALEs]
    F1 --> F3[Predict bystander edits]
    F1 --> F4[Improve parsing]
    E --> G1[TALEN-NT Modernization]
    G1 --> G2[Rewrite in Python 3]
    G1 --> G3[Make importable library]
    G1 --> G4[Remove absolute paths]
    G1 --> G5[Parallelize execution]

    H[Visualization Module] --> I1[Interactive Viewer]
    I1 --> I2[Jandee’s Agent]
    I1 --> I3[JavaScript IGV-like tool]

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