FastQC (Rust)

An unofficial Rust rewrite of FastQC, the sequencing QC tool by Simon Andrews at the Babraham Institute.

Warning

You should probably use the official Java version, not this one.

This project is to be a faithful rewrite of FastQC, with as-close-to identical outputs as possible. The hope is to port improvements back upstream until the rewrite provides no additional functionality or speed. It's basically a development fork in a different language, albeit with a Rust crate for folks building in that ecosystem.

For regular use, it's probably best to stick with the official Java version from Babraham or GitHub.

Why does this exist?

Two reasons, both secondary to the original tool:

• Upstream contributions — a sandbox for prototyping improvements (performance, bug fixes, UI) that get ported back to Java FastQC as PRs. The goal is to make the canonical tool better, not replace it.
• Rust crate — published as fastqc-rust for developers building bioinformatics tooling in the Rust ecosystem. fastqc_data.txt and summary.txt are byte-identical to the Java version — see the equivalence report.

Currently tracking upstream Java FastQC version 0.12.1. See UPSTREAM.toml for details.

Installation + Usage

From a release binary

Download prebuilt binaries from the Releases page.

# Install (Linux x86_64 example -- see docs for all platforms)
curl -fsSL https://github.com/ewels/FastQC-Rust/releases/download/v0.12.1/fastqc-linux-x86_64.tar.gz | tar xz --strip-components=1
sudo mv ./fastqc /usr/local/bin/

# Run
fastqc sample.fastq.gz

Using Docker

docker run ghcr.io/ewels/fastqc-rust:dev fastqc sample.fastq.gz

With Cargo

cargo install fastqc-rust
fastqc sample.fastq.gz

Building from source

# Clone + build
git clone https://github.com/ewels/FastQC-Rust.git
cd FastQC-Rust
cargo build --release

# Run
./target/release/fastqc sample.fastq.gz

Usage

# Analyze a FASTQ file
fastqc sample.fastq.gz

# See all options
fastqc --help

Equivalence testing

This project maintains strict equivalence with the upstream Java FastQC. CI runs automated comparison of text output and chart images against stored Java reference data.

# Run equivalence tests locally (requires uv)
cargo build --release
uv run tests/equivalence/compare.py --binary ./target/release/fastqc

This generates an interactive HTML report with text diffs and side-by-side image comparison. See tests/equivalence/ for details.

Upstream tracking

UPSTREAM.toml pins the Java FastQC version this rewrite tracks. A nightly CI job checks for new upstream releases and automatically creates a GitHub issue when one is found.

License

GPL-3.0 — see LICENSE.

Acknowledgments

FastQC was originally written by Simon Andrews at the Babraham Institute.

Please cite that tool when using outputs from this FastQC-Rust rewrite.