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Focused FASTQ quality-control toolkit

FastQTools

Fast statistics and filtering for FASTQ files, with a CLI for routine QC work and a C++ API for pipeline integration.

Get started CLI reference Benchmarks View on GitHub

Built for researchers and pipeline engineers who want a focused FASTQ tool, not a heavyweight workflow platform.

What you can do with it

  • Inspect sequencing runs quickly

    Use stat for read counts, length distribution, base composition, GC content, and quality summaries in one pass.

  • Filter and trim before downstream steps

    Use filter to combine quality, length, and N-ratio thresholds, then trim low-quality ends without stitching together separate tools.

  • Embed FASTQ processing in C++

    Reuse the public API when you need the same FASTQ primitives inside a larger library or production pipeline.

Start here

If you are trying to… Go to
Build FastQTools and run the first command Getting Started
Check command syntax and examples CLI Reference
Understand the benchmark numbers Benchmark Overview
Integrate the library from C++ API Overview
Build or test the project itself Developer Guide
Contribute docs or code Contributing

Representative benchmarks

FastQTools publishes a compact benchmark snapshot so new users can judge whether the tool fits everyday QC workloads.

Workload Representative result
FASTQ read path 1696 MB/s
FASTQ write path 1.76M reads/s
Combined filtering pass 1.67M reads/s
Full statistics pass 302 MB/s

These figures come from the maintained 100K-read (150 bp) benchmark set on an AMD Ryzen 9 5900X. They are intended as context, not universal promises. See the full benchmark overview for methodology and caveats.

Documentation map

中文概览 · GitHub · MIT License