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bio-read-qc-umi-processing

95 / 100 · Low risk

Fine to try.

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

Extracts UMIs and collapses reads to original molecules with umi_tools (directional dedup) or builds error-corrected single-strand/duplex consensus reads with fgbio. Use when the library has UMIs and accurate molecule counting or below-sequencer-floor error correction is needed - single-cell, low-input RNA-seq, targeted panels, and ctDNA/liquid-biopsy rare-variant detection. For UMI extraction during QC use fastp-workflow; do not dedup non-UMI bulk RNA-seq.

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-read-qc-umi-processing' ] || [ -L ~/.agents/skills/'bio-read-qc-umi-processing' ]; then echo 'A skill folder named bio-read-qc-umi-processing 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 "$d" checkout --quiet '908229c955510a1841b216e8bf58f6b22818d4dc' -- 'skills/bio-read-qc-umi-processing' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bio-read-qc-umi-processing' ~/.agents/skills/'bio-read-qc-umi-processing' && 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-read-qc-umi-processing' ~/.claude/skills/'bio-read-qc-umi-processing' (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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