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@dpatel511 dpatel511 released this 27 Aug 13:32
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v1.0.0
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MetaQuest v1.0.0 - First Stable Release

A Comprehensive Metagenomics Analysis Pipeline

This is the official stable release of MetaQuest - an integrated bioinformatics pipeline that addresses the complex challenges of metagenomic data analysis.

🚀 Key Features

Core Analysis Capabilities

  • Advanced File Validation: Comprehensive FASTQ/FASTA quality control with contamination detection and N50 metrics
  • Taxonomic Classification: Species-level taxonomic profiling with diversity metrics for both FASTQ and FASTA inputs
  • Pathogen Detection: Clinical-grade pathogen screening with risk assessment and comprehensive recommendations
  • Machine Learning Integration: Pre-trained ML models for pathogen prediction with feature extraction and model artifacts
  • Statistical Analysis: Alpha/beta diversity analysis with PERMANOVA, ANOSIM, and differential abundance testing

Analysis Workflows

  • FASTQ Analysis: Rapid Kraken2/Bracken classification optimized for clinical applications
  • FASTA Analysis: High-accuracy BLAST classification with ML enhancement for research applications
  • Comparative Analysis: Multi-sample statistical comparison with publication-ready visualizations

📊 Statistical Testing & Machine Learning

  • Alpha Diversity: Shannon, Simpson, Chao1, and Observed Species metrics with statistical testing
  • Beta Diversity: Bray-Curtis dissimilarity with PCoA visualization
  • Statistical Tests: PERMANOVA and ANOSIM for group comparisons
  • Differential Abundance: Mann-Whitney U tests with FDR and Bonferroni correction
  • ML Biomarker Discovery: Random Forest classification with cross-validation and feature importance

📈 Reporting & Visualization

  • Interactive HTML dashboards with dynamic visualizations
  • Alpha diversity box plots with statistical significance
  • Beta diversity PCoA plots with group clustering
  • Differential abundance volcano plots
  • Interactive taxonomic heatmaps and abundance bar plots
  • Comprehensive statistical comparison summaries

🛠 Installation & Usage

Quick Installation

git clone https://github.com/your-org/metaquest.git
cd metaquest
conda env create -f environment.yml
conda activate metaquest
pip install -e .
metaquest check

Basic Usage Examples

# Validate files
metaquest validate fastq --single sample.fastq.gz
metaquest validate fasta genome.fasta

# Run analysis
metaquest analyze fastq --single sample.fastq.gz -o results/
metaquest analyze fasta genome.fasta -o results/ -s 100

# Compare samples
metaquest compare -i sample1_results/ sample2_results/ -m metadata.tsv -o comparison/

🔬 System Requirements

  • Linux/macOS operating system
  • Conda package manager
  • Minimum 8GB RAM (16GB recommended)
  • 50GB available disk space for databases

📚 Documentation

  • [Installation Guide](installation.md) - Detailed setup instructions
  • [Usage Guide](usage.md) - Comprehensive usage examples and command reference
  • Interactive help system: metaquest --help

🎯 Target Applications

  • Clinical Diagnostics: Pathogen detection and antimicrobial resistance screening
  • Research Applications: Microbiome analysis and comparative genomics
  • Public Health: Outbreak investigation and surveillance
  • Environmental Studies: Microbial community characterization

🔮 Coming Soon (Future Releases)

  • Virulence Factor Analysis (Q3 2025)
  • Enhanced AMR Analysis (Q4 2025)
  • Additional ML models and statistical methods
  • Extended database support

🤝 Contributing

We welcome contributions! See our contributing guidelines for:

  • Machine learning model enhancement
  • Clinical validation studies
  • Additional statistical methods
  • Documentation improvements

📞 Support

  • Bug Reports: Submit via GitHub issues
  • Feature Requests: Use GitHub discussions
  • Documentation: [installation.md](installation.md) and [usage.md](usage.md)

🏆 Acknowledgments

MetaQuest Development Team - Advancing metagenomics through integrated computational solutions

Release Date: August 2025
Version: 1.0.0 (Stable)
License: TBD
Citation: Information will be provided upon publication

This release represents a major milestone with all core functionality complete and thoroughly tested. MetaQuest is ready for production use in both clinical and research environments.

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