bio-alignment-validation

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By BioTender-max/awesome-bio-agent-skills (GitHub) · design · 219 stars · scanned at commit 8cbdd18

Validate alignment quality with insert size distribution, proper pairing rates, GC bias, strand balance, and other post-alignment metrics. Use when verifying alignment data quality before variant calling or quantification.

Works with any agent that supports SKILL.md skills.

What this skill can do

Runs commands on your computer

The author does not mention this.

Found in 18 places.

skills/bioskills/alignment-validation/SKILL.md, line 41samtools quickcheck -v in.bam || echo "QUICKCHECK FAILED"
skills/bioskills/alignment-validation/SKILL.md, line 55test -s in.bam \
skills/bioskills/alignment-validation/SKILL.md, line 64diff \

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skills/bioskills/alignment-validation/SKILL.md, line 76verifybamid2 --SVDPrefix /resources/1000g.b38.vcf.gz.SVD \
skills/bioskills/alignment-validation/SKILL.md, line 102samtools stats input.bam > stats.txt
skills/bioskills/alignment-validation/SKILL.md, line 109java -jar picard.jar CollectInsertSizeMetrics \
skills/bioskills/alignment-validation/SKILL.md, line 173samtools flagstat input.bam
skills/bioskills/alignment-validation/SKILL.md, line 181proper=$(samtools view -c -f 2 input.bam)
skills/bioskills/alignment-validation/SKILL.md, line 202java -jar picard.jar CollectGcBiasMetrics \
skills/bioskills/alignment-validation/SKILL.md, line 213computeGCBias \
skills/bioskills/alignment-validation/SKILL.md, line 236forward=$(samtools view -c -F 16 input.bam)
skills/bioskills/alignment-validation/SKILL.md, line 247for chr in chr1 chr2 chr3; do
skills/bioskills/alignment-validation/SKILL.md, line 259samtools view input.bam | cut -f5 | sort -n | uniq -c | sort -k2 -n
skills/bioskills/alignment-validation/SKILL.md, line 265samtools view input.bam | awk '{sum+=$5; count++} END {print "Mean MAPQ:", sum/count}'
skills/bioskills/alignment-validation/SKILL.md, line 277samtools idxstats input.bam | awk '{print $1, $3/$2}' | head -25
skills/bioskills/alignment-validation/SKILL.md, line 284samtools idxstats in.bam | awk '$2>0 && $1!~/^chr[XYM]|^GL|^KI|^chrUn|^chrEBV/ {
skills/bioskills/alignment-validation/SKILL.md, line 301java -jar picard.jar CollectAlignmentSummaryMetrics \
skills/bioskills/alignment-validation/SKILL.md, line 324BAM=$1

Connects to the internet

The author does not mention this.

Found in 5 places.

skills/bioskills/alignment-validation/SKILL.md, line 147for i, read in enumerate(bam.fetch()):
skills/bioskills/alignment-validation/examples/validate_alignment.py, line 25for i, read in enumerate(bam.fetch()):
skills/bioskills/alignment-validation/usage-guide.md, line 159for i, read in enumerate(bam.fetch()):

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skills/bioskills/alignment-validation/usage-guide.md, line 189for i, read in enumerate(self.bam.fetch()):
skills/bioskills/alignment-validation/usage-guide.md, line 200for i, read in enumerate(self.bam.fetch()):

Downloads and installs other software

The author does not mention this.

Found in 1 place.

skills/bioskills/alignment-validation/usage-guide.md, line 12pip install pysam numpy matplotlib

Safer alternatives

Low-risk skills in the same category (design) 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-alignment-validation' ] || [ -L ~/.agents/skills/'bio-alignment-validation' ]; then echo 'A skill folder named bio-alignment-validation already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/BioTender-max/awesome-bio-agent-skills' "$d" && git -C "$d" checkout --quiet '8cbdd18837aa6296c4e77616a03b323bd69b57b1' -- 'skills/bioskills/alignment-validation' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bioskills/alignment-validation' ~/.agents/skills/'bio-alignment-validation' && 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-alignment-validation' ~/.claude/skills/'bio-alignment-validation' (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
2026-11-07	`8cbdd18`	75