FastQTools

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Online Docs: https://lessup.github.io/fastq-tools/

A modern C++ high-performance FASTQ file processing toolkit for bioinformatics QC, filtering, and statistical analysis.

Quick Start

# One-click build
./scripts/core/build

# View help
./build/release/bin/fqtools --help

# Quality control
./build/release/bin/fqtools qc -i input.fastq -o report.json

# Filtering
./build/release/bin/fqtools filter -i input.fastq -o output.fastq -q 20 -l 50

Features

• Quality Control — Per-base/per-read quality statistics, GC content, length distribution
• Read Filtering — Quality threshold, length range, N-ratio, complexity filtering
• Statistics — Comprehensive FASTQ metrics with JSON/HTML reports
• High Performance — Multi-threaded I/O, SIMD-accelerated quality parsing
• Modern C++ — C++23, CMake 3.20+, Conan 2.x dependencies

Tech Stack

• C++23, CMake 3.20+, Conan 2.x
• Google Test, Google Benchmark
• zlib (compressed FASTQ support)

Build

# Install dependencies
conan install . --build=missing -of=build

# Build
cmake --preset release
cmake --build build/build/Release -j$(nproc)

# Run tests
ctest --test-dir build/build/Release

Project Structure

fastq-tools/
├── src/                # Source code
│   ├── core/           # Core library (parser, filter, stats)
│   ├── cli/            # CLI entry point
│   └── io/             # I/O layer (buffered, compressed)
├── include/            # Public headers
├── tests/              # Unit & integration tests
├── benchmarks/         # Performance benchmarks
├── scripts/            # Build & utility scripts
└── docs/               # Documentation

License

MIT License