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snipe

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snipe is an alignment-free QC tool for sequencing data. It sketches reads or genomes into k-mer-pair signatures and computes quality metrics — coverage, depth, error and mutation rates, contamination — equivalent to those from an alignment-based QC tool such as qualimap, but without aligning reads (no aligner, no BAM).

This is the ten-minute path: install snipe, sketch a genome, inspect a signature, and run QC. Every output on this page is captured from a real run on the bundled phiX174 genome — copy the commands and you’ll see the same numbers.

  1. Install snipe.

    Terminal window
    pip install snipe

    This installs the snipe command. For source builds, feature flags (SRA), and the platform matrix, see Installation.

  2. Sketch a genome.

    We’ll use the phiX174 genome ({captured.input}). At --scale 1 snipe keeps every k-mer — the right choice for a tiny input, so nothing is sampled away.

    Terminal window
    snipe sketch --sample phix.fasta -o phix.snipesig --scale 1

    This writes phix.snipesig — the native, Parquet-encoded signature format.

  3. Inspect it.

    Terminal window
    snipe info phix.snipesig
    snipe info phix.snipesig
    
=== Signature Information ===
Version: 2.0.0
Created: <at sketch time>
K1 length: 51
K2 length: 53
K2 extension length: 2 bases
Scale: 1
Hash threshold: 18446744073709551615
Hash space coverage: 100.000000%
Theoretical sampling rate: 1/1 = 1.000000

=== Input Files ===
  1: phix.fasta

=== K-mer Statistics ===
Unique K1 k-mers: 5336
Total K1 abundance: 5336
Average K1 abundance: 1.00
Unique K2 k-mers: 5334
Total K2 abundance: 5334
Average K2 abundance: 1.00
Unique k-mer edgemers: 5334
Total edgemer abundance: 5334
Average pair abundance: 1.00
K1 checksum (md5): 85e65cc582d48cbf2fa1b2b7c9b552c7
K2 checksum (md5): 91adce917f75e09fb1d6790e1619d446
Failed K2 pairs: 2 (total abundance: 2)
K2 extension success rate: 99.96%
K1s processed for K2 extension: 5336

=== Processing Statistics ===
Processing time: 0.02s
Sequences processed: 1
Total bases processed: 5386
Average sequence length: 5386.0 bp
K1 positions examined: 5336
K1 hashes generated: 5336
K1 hashes below threshold: 5336
K1 hashes above threshold: 0
Hash efficiency: 100.00%
K1 with valid extensions: 5334
K1 without extension space: 2

    That’s the whole model in one screen: the K1/K2 sizes, the FracMinHash Scale, and the edgemer counts — here 5336 unique K1 k-mers and 5334 edgemer pairs.

  4. Run QC against a reference.

    Sketch the same genome as a reference, then score the sample against it:

    Terminal window
    snipe qc --reference phix_ref.snipesig --sample phix.snipesig -o qc.tsv

    This writes a qc.tsv with dozens of quality metrics (coverage, error and mutation rates, chromosome depths, contamination). Browse them all in the QC metrics catalog.

Next steps

Section titled “Next steps”