Guides

Step-by-step guides for common snipe tasks. New here? Start with Get started for the ten-minute path, then pick a guide.

snipe runs quality control on sequencing data without aligning reads: it sketches the input and computes coverage, depth (overall and per chromosome), error and mutation rates, contamination, and sex-chromosome signals — the metrics an alignment-based QC tool such as qualimap reports, computed from a sketch instead of a BAM.

Sketch a genomeTurn a FASTA into a .snipesig — reference vs. sample, scale, and inspection.

QC a sequencing runScore a sample against a reference and read the quality metrics — no alignment required.

Compare samplesIntersect, union, sum, and diff signatures — CLI and Python operators.

ReproducibilityThe same input produces the same signature — same checksum on every run.

Working with sourmashOptional interop: round-trip a snipe sketch to a sourmash .sig at the K1 level.