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bio-read-alignment-bowtie2-alignment

95 / 100 · Low risk

Fine to try.

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

Aligns DNA short reads to a reference with Bowtie2, choosing end-to-end (whole read must align) vs local (soft-clip read ends) mode and a sensitivity preset; the de-facto aligner for ChIP-seq, ATAC-seq, and CUT&RUN, where fragment-geometry flags (--no-mixed, --no-discordant, --dovetail, -X) and a tool-appropriate MAPQ filter feed the peak caller. Use when aligning ChIP/ATAC/CUT&RUN reads, when read ends are adapter-contaminated and need soft-clipping, or when a tunable sensitivity/speed preset …

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-alignment-bowtie2-alignment' ] || [ -L ~/.agents/skills/'bio-read-alignment-bowtie2-alignment' ]; then echo 'A skill folder named bio-read-alignment-bowtie2-alignment 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 "$d" checkout --quiet '908229c955510a1841b216e8bf58f6b22818d4dc' -- 'skills/bio-read-alignment-bowtie2-alignment' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bio-read-alignment-bowtie2-alignment' ~/.agents/skills/'bio-read-alignment-bowtie2-alignment' && 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-alignment-bowtie2-alignment' ~/.claude/skills/'bio-read-alignment-bowtie2-alignment' (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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