rustqc 0.1.0

Fast RNA-seq QC in a single pass: dupRadar, featureCounts, 8 RSeQC tools, preseq, samtools stats, and Qualimap — reimplemented in Rust
rustqc-0.1.0 is not a library.

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

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

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

License

MIT License. See LICENSE for details.