Bioquik Documentation

Welcome to Bioquik, a high-performance toolkit for counting DNA sequence motifs across large FASTA datasets.

Bioquik is designed for batch analysis. It processes directories of FASTA files in parallel and writes results to disk as CSV, JSON, and optional plots.

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Installation

pip install bioquik

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Quickstart

See the Quickstart guide for command-line and Python examples.

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Contents

Tutorials

• Quickstart
  • Command-line usage
  • Python usage
  • Single-file processing (advanced)
• Validation
  • Directory validation
  • Pattern validation
  • Common mistakes
• Reports
  • Per-file motif counts
  • Combined reports
  • Writing summaries
  • Plots

Architecture

• Architecture Guide
  • System Overview
  • Core Components
  • Data Flow
  • Memory Management
  • Performance Characteristics
  • Extension Points
  • Design Decisions
  • Testing Strategy
  • Future Enhancements
  • Further Reading

API Reference

• bioquik
  • bioquik package