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Getting Started

This guide helps you set up FastQTools and run your first command in minimal time.

System Requirements

Runtime (Minimum)

  • Ubuntu 20.04+ or Debian 11+
  • 1GB RAM / 100MB disk
  • Ubuntu 22.04+ or Debian 12+
  • 4GB RAM / 2GB disk
  • Multi-core CPU (speeds up parallel builds)

Install Dependencies

# Development environment (compilers, build tools, debug tools)
./scripts/core/install-deps

# Runtime only (production deployment)
./scripts/core/install-deps --runtime

# Show help
./scripts/core/install-deps --help

Development dependencies include:

  • GCC 15 / Clang 21 compilers
  • CMake, Ninja build system
  • Conan 2.x package manager
  • GDB, Valgrind debugging tools
  • lcov coverage tool

Runtime dependencies include:

  • libtbb12 (Intel TBB parallel library)
  • zlib, bzip2, xz compression libraries
  • libdeflate (high-performance decompression)

Build

# Default build (Clang + Release)
./scripts/core/build

# Development mode (Debug + verbose output)
./scripts/core/build --dev

# Specify compiler and build type
./scripts/core/build --compiler gcc --type Debug

# Show all options
./scripts/core/build --help

After a successful build, the executable is at build/clang-release/FastQTools (or the corresponding build directory).

Verify Installation

# Show help
./build/clang-release/FastQTools --help

# Run tests
./scripts/core/test

First Example

1. Prepare Test Data

# Generate test FASTQ file
python3 tools/data/gen_fastq.py -o test_data.fastq --reads 5000 --min-len 80 --max-len 150

2. Statistical Analysis

FastQTools stat -i test_data.fastq -o stats.txt --threads 4

Output includes: total reads, length distribution, base composition (A/T/C/G/N), GC content, Q20/Q30 percentages, etc.

3. Quality Filtering

FastQTools filter -i test_data.fastq -o filtered.fastq \
  --min-quality 20 \
  --min-length 50 \
  --max-n-ratio 0.1 \
  --trim-quality 20 \
  --trim-mode both

Troubleshooting

Dependency installation fails

  • Ensure system is Ubuntu/Debian-based
  • Manually update package list: sudo apt-get update
  • Check network connectivity

Build fails

  • Confirm Conan is installed: conan --version
  • Confirm CMake is available: cmake --version
  • Confirm compiler is available: clang++ --version or g++ --version

Executable not found

  • Check build directory: ls build/clang-release/FastQTools
  • Confirm build script completed successfully (exit code 0)

Missing shared libraries at runtime

# Check missing libraries
ldd build/clang-release/FastQTools

# Install runtime dependencies
./scripts/core/install-deps --runtime

Next Steps