microflex 0.1.0

Cross-platform Python toolkit for microbiome analysis using multiple sequencing technologies

microflex

A cross-platform Python toolkit for microbiome analysis using multiple sequencing technologies including Illumina (NGS), Oxford Nanopore, and Sanger sequencing.

Features

• Multi-platform support: Illumina NGS, Oxford Nanopore, Sanger sequencing
• Multiple input formats: .fastq, .fasta, .ab1, .qza, .biom
• Comprehensive preprocessing: Quality control, trimming, chimera detection
• Taxonomic classification: BLAST, Kraken2, QIIME2 integration
• Ecological analysis: Alpha/beta diversity, ordination, clustering
• Functional predictions: PICRUSt2 and HUMAnN2 support
• Rich visualizations: Interactive and static plots
• Automated reporting: PDF/HTML reports
• Modular design: Use only what you need

Installation

From PyPI (recommended)

pip install microflex

Development installation

git clone https://github.com/ataozsoysoy/microflex.git
cd microflex
pip install -e ".[dev]"

Optional dependencies

# For web interface
pip install "microflex[web]"

# For documentation
pip install "microflex[docs]"

# All optional dependencies
pip install "microflex[dev,web,docs]"

Quick Start

Python API

from microflex.io import FastqReader
from microflex.preprocess import QualityFilter
from microflex.taxonomy import MockClassifier
from microflex.analysis import DiversityAnalyzer

# Read sequencing data
reader = FastqReader()
sequences = reader.read("data/samples.fastq")

# Quality filtering
quality_filter = QualityFilter(min_quality_score=20, min_length=100)
filtered_sequences = quality_filter.process(sequences)

# Taxonomic classification
classifier = MockClassifier(confidence_range=(70.0, 95.0))
taxonomy_results = classifier.process(filtered_sequences)

# Diversity analysis
analyzer = DiversityAnalyzer()
alpha_metrics = analyzer.calculate_alpha_diversity(abundance_data)
beta_distances = analyzer.calculate_beta_diversity(abundance_matrix)

Command Line Interface

# Get file information
python -m microflex.cli.main info sequences.fastq

# Filter sequences by quality
python -m microflex.cli.main filter sequences.fastq --min-length 100 --min-quality 20

# Taxonomic classification
python -m microflex.cli.main classify sequences.fasta --method mock

# Diversity analysis
python -m microflex.cli.main analyze taxonomy.tsv --level genus

# Convert between formats
python -m microflex.cli.main convert sequences.fastq --format fasta

Available CLI Commands

Command	Description	Example
info	Display file information	python -m microflex.cli.main info sequences.fastq
filter	Quality-based sequence filtering	python -m microflex.cli.main filter sequences.fastq --min-length 100
classify	Taxonomic classification	python -m microflex.cli.main classify sequences.fasta --method mock
analyze	Diversity analysis	python -m microflex.cli.main analyze taxonomy.tsv --level genus
convert	Format conversion	python -m microflex.cli.main convert sequences.fastq --format fasta

Project Structure

microflex/
├── src/microflex/
│   ├── core/           # Core abstractions and interfaces
│   ├── io/             # Input/output handlers
│   ├── preprocess/     # Quality control and preprocessing
│   ├── taxonomy/       # Taxonomic classification
│   ├── analysis/       # Ecological analysis
│   ├── functional/     # Functional predictions
│   ├── visualization/  # Plotting and visualization
│   ├── cli/            # Command line interface
│   └── utils/          # Utilities and helpers
├── tests/              # Test suite
├── docs/               # Documentation
└── examples/           # Example scripts and notebooks

Documentation

Full documentation is available at microflex.readthedocs.io

Contributing

We welcome contributions! Please see our Contributing Guide for details.

Development Setup

# Clone the repository
git clone https://github.com/ataozsoysoy/microflex.git
cd microflex

# Create virtual environment
python -m venv venv
source venv/bin/activate  # On Windows: venv\Scripts\activate

# Install in development mode
pip install -e ".[dev]"

# Install pre-commit hooks
pre-commit install

# Run tests
pytest

# Run linting
black src/ tests/
isort src/ tests/
flake8 src/ tests/
mypy src/

License

This project is licensed under the MIT License - see the LICENSE file for details.

Citation

If you use microflex in your research, please cite:

@software{microflex,
  author = {Özsoy, Ata Umut},
  title = {microflex: Cross-platform Python toolkit for microbiome analysis},
  url = {https://github.com/ataozsoysoy/microflex},
  version = {0.1.0},
  year = {2025}
}

Roadmap

• v0.1.0: Core architecture, I/O modules, quality filtering, mock classification, alpha/beta diversity, CLI
• v0.2.0: BLAST integration, Kraken2 support, visualization module
• v0.3.0: Nanopore support, PICRUSt2 integration, web interface
• v1.0.0: Stable release with comprehensive documentation and tutorials

Support

• 📖 Documentation
• 🐛 Issue Tracker
• 💬 Discussions

Acknowledgments

Special thanks to the bioinformatics community and the developers of the underlying tools that make microflex possible.