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bio-workflows-metagenomics-pipeline

95 / 100 · Low risk

Fine to try.

By lilinji/GeneTind-Life-Skills (GitHub) · productivity · 17 stars · scanned at commit 908229c

End-to-end shotgun metagenomics workflow from FASTQ to taxonomic and functional profiles, orchestrating controls/host depletion, Kraken2+Bracken classification, MetaPhlAn marker profiling, and HUMAnN functional profiling. Covers the controls-first ordering, why Kraken2 read counts are not abundances and MetaPhlAn cell fractions do not equal Bracken read fractions, and the consistent-pipeline framing. Use when profiling shotgun metagenomic samples end to end, or chaining classification, abundanc…

Works with any agent that supports SKILL.md skills.

What this skill can do

Install

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

if [ -e ~/.agents/skills/'bio-workflows-metagenomics-pipeline' ] || [ -L ~/.agents/skills/'bio-workflows-metagenomics-pipeline' ]; then echo 'A skill folder named bio-workflows-metagenomics-pipeline already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/lilinji/GeneTind-Life-Skills' "$d" && git -C "$d" checkout --quiet '908229c955510a1841b216e8bf58f6b22818d4dc' -- 'skills/bio-workflows-metagenomics-pipeline' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bio-workflows-metagenomics-pipeline' ~/.agents/skills/'bio-workflows-metagenomics-pipeline' && 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/'bio-workflows-metagenomics-pipeline' ~/.claude/skills/'bio-workflows-metagenomics-pipeline' (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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