CLI reference

The snipe command has 12 subcommands. Every page below is generated directly from the CLI, so it can never drift from the tool.

snipe differenceCompute the difference (first minus the rest) of signatures.

snipe downscaleDownscale a signature to a larger scale (fewer k-mers).

snipe exportExport a signature to sourmash / snipe-sig / a human-readable TSV directory.

snipe guided-mergeMerge signatures by experiment groups specified in a TSV file.

snipe infoDisplay detailed information about one or more signatures.

snipe intersectCompute the edgemer intersection of a sample and a reference signature.

snipe kmers2readsReconstruct k-mer read sequences from a --keep-acgt signature into FASTA.

snipe pangenomePangenome analysis: identify core and accessory k-mers across samples.

snipe qcCompute quality-control metrics for sample signatures against a reference.

snipe sketchCreate a k-mer sketch signature from sample reads or a genome reference.

snipe sumSum abundances across two or more signatures.

snipe unionCompute the union (max-merge) of two or more signatures.