rsomics-fastq-downsample

Deterministic random downsampling of a FASTQ file to a target fraction of its reads. Each read is kept by an independent Bernoulli trial seeded by --seed, so a given seed and fraction always select the same reads.

Install

cargo install rsomics-fastq-downsample

Usage

# keep ~10% of reads, reproducibly
rsomics-fastq-downsample reads.fq -f 0.1 --seed 42 -o sub.fq

# keep half the reads
rsomics-fastq-downsample reads.fq -f 0.5 --seed 7

# fraction 1.0 keeps everything (still streams through the sampler)
rsomics-fastq-downsample reads.fq -f 1.0 --seed 1 -o out.fq

• -f, --fraction — fraction of reads to keep, 0.0-1.0 (default 0.1).
• -o, --output — output path (- = stdout).
• --seed — RNG seed for reproducible selection.

This is a per-read Bernoulli sampler: the number of surviving reads is close to fraction x N but not exactly fixed. For an exact target count use rsomics-fastq-sample -n.

Origin

Independent Rust reimplementation of fraction-based FASTQ downsampling as done by seqtk sample and seqkit sample -p, based on the tools' documented behaviour and black-box comparison: with the same fraction the retained-read count is comparable to both upstreams (an independent RNG cannot reproduce the exact reads either tool selects, so agreement is at the fraction level, not byte-for-byte). Test fixtures are independently generated.

License: MIT OR Apache-2.0. Upstream credit: seqtk (MIT), seqkit (MIT).