← All skills

bio-genome-assembly-contamination-detection

75 / 100 · Review before installing

Check before installing.

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

Detects and removes contamination in genome assemblies via two disjoint workflows - foreign-sequence screening of a single-organism (eukaryote/isolate) assembly with NCBI FCS-GX (GenBank-submission-mandatory), FCS-adaptor, and BlobToolKit blob plots; and MAG/bin quality assessment with CheckM2 plus GUNC (chimerism) plus GTDB-Tk taxonomy, judged against MIMAG. Covers why CheckM2 alone is blind to disjoint-marker chimeras, the FCS-GX RAM wall, organelle/NUMT triage, strain heterogeneity, and the …

Works with any agent that supports SKILL.md skills.

What this skill can do

Safer alternatives

Low-risk skills in the same category (other) that look related. Check that one does what you need.

• 80 Low riskbio-genome-assembly-assembly-qcdiegosouzapw/awesome-omni-skill · 66 stars
• 95 Low riskgenomics-assemblymdbabumiamssm/LLMs-Universal-Life-Science-and-Clinical-Skills- · 36 stars
• 95 Low riskgenome-assembly-pipelinemdbabumiamssm/LLMs-Universal-Life-Science-and-Clinical-Skills- · 36 stars

Install

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

if [ -e ~/.agents/skills/'bio-genome-assembly-contamination-detection' ] || [ -L ~/.agents/skills/'bio-genome-assembly-contamination-detection' ]; then echo 'A skill folder named bio-genome-assembly-contamination-detection 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 "$d" checkout --quiet '908229c955510a1841b216e8bf58f6b22818d4dc' -- 'skills/bio-genome-assembly-contamination-detection' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bio-genome-assembly-contamination-detection' ~/.agents/skills/'bio-genome-assembly-contamination-detection' && 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-genome-assembly-contamination-detection' ~/.claude/skills/'bio-genome-assembly-contamination-detection' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.

Badge for your README

The badge for lilinji/GeneTind-Life-Skills shows the score of its lowest-scoring skill.

[![SkillTrust](https://zalavijaysinh.github.io/skilltrust/badges/lilinji/GeneTind-Life-Skills.svg)](https://zalavijaysinh.github.io/skilltrust/repos/lilinji/GeneTind-Life-Skills/)

Score history