sourmash

80 / 100 · Low risk

Fine to try.

By stanfish06/skillquarium (GitHub) · productivity · 12 stars · scanned at commit f748ea9

MinHash/FracMinHash sketching for alignment-free comparison of genomes and metagenomes. Use for fast all-vs-all genome similarity and ANI estimation across thousands of genomes without alignment, taxonomic classification of metagenomes against GTDB/NCBI reference databases (sourmash gather/tax), and sequencing-cohort QC (contamination or duplicate detection). Complements upstream assembly/QC pipelines (snakemake-workflow-engine, nextflow) and feeds downstream phylogenetics; distinct from alignm…

Works with any agent that supports SKILL.md skills.

What this skill can do

Downloads and installs other software

The author does not mention this.

Found in 3 places.

skills/sourmash/SKILL.md, line 10compatibility: Requires Python 3.11+ and sourmash 4.x (current 4.9.4). The core is a Rust extension distributed as prebuilt wheels via pip/conda; building from
skills/sourmash/SKILL.md, line 30uv pip install sourmash
skills/sourmash/SKILL.md, line 33uv pip install sourmash_plugin_branchwater

Runs commands on your computer

The author does not mention this.

Found in 6 places.

skills/sourmash/SKILL.md, line 26conda create -n sourmash_env -c conda-forge sourmash-minimal
skills/sourmash/SKILL.md, line 59sourmash sketch dna -p k=31,scaled=1000 *.fa.gz
skills/sourmash/SKILL.md, line 73sourmash compare genome1.sig genome2.sig --estimate-ani -o ani_results.csv

Show 3 more

skills/sourmash/SKILL.md, line 82sourmash gather metagenome.sig gtdb-rs214-k31.zip -o gather_results.csv
skills/sourmash/SKILL.md, line 93sourmash sketch dna -p k=31,scaled=1000 reference_genomes/*.fa.gz
skills/sourmash/SKILL.md, line 104sourmash sketch dna -p k=31,scaled=1000 sample*.fq.gz

Install

Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.

if [ -e ~/.agents/skills/'sourmash' ] || [ -L ~/.agents/skills/'sourmash' ]; then echo 'A skill folder named sourmash already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/stanfish06/skillquarium' "$d" && git -C "$d" checkout --quiet 'f748ea91aa51ce8fc42c27c809dba73a8377b1d5' -- 'skills/sourmash' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/sourmash' ~/.agents/skills/'sourmash' && rm -rf "$d"; fi

Codex reads ~/.agents/skills directly. For Claude Code, Cursor, Copilot, Gemini CLI, Antigravity or OpenCode, also link it. For Claude Code: ln -s ~/.agents/skills/'sourmash' ~/.claude/skills/'sourmash' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.

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Score history

Date	Version	Score
2026-11-08	`f748ea9`	80