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Sourmash signature compare starter

Skill ma-compbio-lab/SkillFoundry/skills/genomics/sourmash-signature-compare-starter

A framework for discovering, compiling, and validating reusable skills for scientific agents.

Install
npx -y skills add ma-compbio-lab/SkillFoundry --skill sourmash-signature-compare-starter

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SKILL.md

1.1 KB, 257 tokens by cl100k_base, as published. Nobody here has run it

sourmash Signature Compare Starter

Use this skill to compute deterministic MinHash signatures for two tiny DNA sequences with sourmash and summarize their similarity in compact JSON.

What it does

  • Reads two small FASTA inputs.
  • Computes sourmash MinHash sketches with fixed ksize and scaled.
  • Reports hash counts, shared-hash count, Jaccard similarity, and pairwise containment.

When to use it

  • You need a local, no-auth starter for metagenomics-style sketch comparison.
  • You want a minimal example of sourmash sequence sketching without a large database.
  • You want a deterministic JSON artifact for downstream tests or demos.

Example

slurm/envs/metagenomics/bin/python skills/genomics/sourmash-signature-compare-starter/scripts/run_sourmash_signature_compare.py \
  --out scratch/metagenomics/sourmash_compare_summary.json

Verification

  • Skill-local tests: python3 -m unittest discover -s skills/genomics/sourmash-signature-compare-starter/tests -p 'test_*.py'
  • Expected summary: shared_hash_count == 12 and jaccard_similarity == 0.631579

Keep looking

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