bio-cfdna-preprocessing

77 / 100 · Review before installing

Check before installing. Some of what it can do is expected: a data skill usually connects to databases or online services with your credentials.

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

Decides how to preprocess plasma cfDNA sequencing data so the recoverable signal survives - library-prep-aware fragment expectations (dsDNA vs ssDNA/adaptase prep), UMI/duplex consensus with fgbio (ExtractUmisFromBam, GroupReadsByUmi --strategy paired for duplex, CallMolecularConsensusReads vs CallDuplexConsensusReads, FilterConsensusReads min-reads "total s1 s2"), the align->group->consensus->RE-align ordering, and the cfDNA dedup trap where naive coordinate dedup collapses nucleosome-coincide…

Works with any agent that supports SKILL.md skills.

What this skill can do

Runs commands on your computer

This is disclosed by the author in the skill's SKILL.md or README.

Found in 5 places.

skills/bio-cfdna-preprocessing/SKILL.md, line 66fgbio ExtractUmisFromBam --input raw.unmapped.bam --output with_umis.bam \
skills/bio-cfdna-preprocessing/examples/preprocess_cfdna.py, line 18subprocess.run(cmd, check=True)
skills/bio-cfdna-preprocessing/examples/preprocess_cfdna.py, line 41subprocess.run(f'bwa mem -t {threads} -Y {reference} {with_umis} | samtools sort -o {aligned} -',

Show 2 more

skills/bio-cfdna-preprocessing/examples/preprocess_cfdna.py, line 42shell=True, check=True)
skills/bio-cfdna-preprocessing/examples/preprocess_cfdna.py, line 60subprocess.run(realign, shell=True, check=True)

Connects to the internet

The author does not mention this. Expected for a data skill.

Found in 2 places.

skills/bio-cfdna-preprocessing/SKILL.md, line 111sizes = [r.template_length for r in bam.fetch()
skills/bio-cfdna-preprocessing/examples/preprocess_cfdna.py, line 84sizes = [r.template_length for r in bam.fetch()

Downloads and installs other software

The author does not mention this.

Found in 1 place.

skills/bio-cfdna-preprocessing/usage-guide.md, line 9pip install pysam numpy

Safer alternatives

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

Install

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

if [ -e ~/.agents/skills/'bio-cfdna-preprocessing' ] || [ -L ~/.agents/skills/'bio-cfdna-preprocessing' ]; then echo 'A skill folder named bio-cfdna-preprocessing 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 "$d" checkout --quiet '908229c955510a1841b216e8bf58f6b22818d4dc' -- 'skills/bio-cfdna-preprocessing' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bio-cfdna-preprocessing' ~/.agents/skills/'bio-cfdna-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/'bio-cfdna-preprocessing' ~/.claude/skills/'bio-cfdna-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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Score history

Date	Version	Score
2026-11-11	`908229c`	77