Fast genomics quality control tools for sequencing data, written in Rust.

Documentation • Quickstart • Benchmarks • Releases

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RustQC is a suite of fast QC tools for sequencing data, compiled to a single static binary with no runtime dependencies.

Run time for a large paired-end RNA-seq BAM (~186M reads) on AWS.

It currently includes:

• rustqc rna is a single-command RNA-Seq QC tool that runs all QC analyses in one pass. Designed to slot into the nf-core/rnaseq pipeline, but works anywhere:

Tool	Reimplements	Description
dupRadar	dupRadar	PCR duplicate rate vs. expression analysis with density scatter plots
featureCounts	featureCounts	Gene-level read counting with biotype summaries
bam_stat	RSeQC bam_stat.py	Basic alignment statistics
infer_experiment	RSeQC infer_experiment.py	Library strandedness inference
read_duplication	RSeQC read_duplication.py	Position- and sequence-based duplication histograms
read_distribution	RSeQC read_distribution.py	Read distribution across genomic features
junction_annotation	RSeQC junction_annotation.py	Splice junction classification
junction_saturation	RSeQC junction_saturation.py	Splice junction saturation analysis
inner_distance	RSeQC inner_distance.py	Paired-end inner distance distribution
TIN	RSeQC tin.py	Transcript Integrity Number
preseq	preseq lc_extrap	Library complexity extrapolation
Qualimap rnaseq	Qualimap rnaseq	Gene body coverage, read origin, strand specificity
flagstat	samtools flagstat	Alignment flag summary
idxstats	samtools idxstats	Per-chromosome read counts
stats	samtools stats	Full samtools stats output including all histogram sections

All outputs are format- and numerically identical to the upstream tools, and compatible with MultiQC for reporting.

Quick start

# Install (Linux x86_64 example -- see docs for all platforms)
curl -fsSL https://github.com/seqeralabs/RustQC/releases/latest/download/rustqc-linux-x86_64.tar.gz | tar xz --strip-components=1
sudo mv ./rustqc /usr/local/bin/

# Run RNA-Seq QC
rustqc rna sample.markdup.bam --gtf genes.gtf --paired --outdir results/

# Or use Docker
docker run --rm -v "$PWD":/data ghcr.io/seqeralabs/rustqc:latest \
  rustqc rna /data/sample.markdup.bam --gtf /data/genes.gtf --outdir /data/results

# Or install from crates.io
cargo install rustqc

See the documentation for full usage details, configuration options, output file descriptions, and benchmark results.

AI & Provenance

RustQC was developed with substantial assistance from AI coding agents (primarily Claude), using the upstream tool source code as reference. Correctness is validated by comparing output against the original tools on real sequencing data, not by manual code review alone. See the AI & Provenance documentation for full details, including known validation gaps.

License

This project is licensed under the GNU General Public License v3.0 or later. See LICENSE for details.