snipe
alignment-free QC · edgemer sketching
Sequencing QC, without the alignment.
snipe sketches sequencing data into compact edgemer signatures and reports the quality metrics you'd get from aligning reads and running a tool like qualimap — coverage, depth, error and mutation rates — without aligning a single read. The same input produces the same output.
pip install snipethen snipe sketch --help.snipesig signature.QCScore a sample against a reference — 60+ metrics.CompareIntersect, union, and diff signatures.ExportWrite to TSV, sourmash .sig, and more.Why snipe
Section titled “Why snipe”snipe reports sequencing quality-control metrics — coverage, depth (overall and per chromosome), error and mutation rates, contamination, and sex-chromosome signals — without aligning reads to a reference. It works from a compact sketch rather than a BAM, answering the same questions an alignment-based QC tool such as qualimap answers, but without an aligner.
The sketch is built from edgemers: k-mer pairs in which a base k-mer (K1, default 51 bp) sits centred inside a longer k-mer (K2, default 53 bp) that extends one base on each side. Reads that match at K1 but not at K2 separate likely sequencing errors from true variation.
- No alignment. QC runs from a
.snipesigsketch — no aligner and no BAM. - QC metrics. 60+ metrics spanning coverage, contamination, ploidy, chromosome depth, and error and mutation rates, in default /
--advanced/--hiddentiers. - CLI and Python API. A Typer CLI and a Python API call the same Rust core.
The native .snipesig format is Parquet-encoded; the same input produces the same output (same checksum).
Retrieval-only — every answer links to the source. Runs entirely in your browser.