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fastp-fastq-preprocessing

95 / 100 · Low risk

Fine to try.

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

All-in-one FASTQ QC and adapter trimming. Auto-detects Illumina adapters, filters low-quality reads, corrects paired-end overlaps, emits HTML+JSON QC in one pass. 3-10x faster than Trim Galore/Trimmomatic. First step before STAR, BWA-MEM2, or Salmon.

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/'fastp-fastq-preprocessing' ] || [ -L ~/.agents/skills/'fastp-fastq-preprocessing' ]; then echo 'A skill folder named fastp-fastq-preprocessing 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 "$d" checkout --quiet 'f748ea91aa51ce8fc42c27c809dba73a8377b1d5' -- 'skills/fastp-fastq-preprocessing' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/fastp-fastq-preprocessing' ~/.agents/skills/'fastp-fastq-preprocessing' && 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/'fastp-fastq-preprocessing' ~/.claude/skills/'fastp-fastq-preprocessing' (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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