dino-quant

Experimental quantized DNA sketch prefilters for sequence-search pipelines.

dino-quant compresses DNA k-mer sketch vectors into small approximate codes, uses those codes to route reads to likely reference windows, and emits candidate ranges for downstream exact tools. It is a prefilter: exact alignment, classification, and biological interpretation stay outside this crate.

Commands

cargo run -p dino-quant --release -- demo
cargo run -p dino-quant --release -- bench-fasta reference.fa.gz
cargo run -p dino-quant --release -- emit-candidates reference.fa reads.fastq
cargo run -p dino-quant --release -- emit-candidate-reference reference.fa candidates.tsv
cargo run -p dino-quant --release -- emit-protein-candidates proteins.faa queries.faa
cargo test -p dino-quant

Scope

dino-seq is the only FASTA/FASTQ input backend. Quantized candidates are a prefilter only; exact alignment stays downstream.

emit-candidates writes target_id with each row so emit-candidate-reference can reconstruct multi-record references even when FASTA headers share the same first token. Minimizer reference caches are tied to the parsed reference content and are rebuilt automatically when that content changes.

Retrieval Modes

Release Checks

cargo fmt --all --check
cargo test -p dino-quant
cargo clippy -p dino-quant --all-targets -- -D warnings
cargo package -p dino-quant --allow-dirty --list