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alignment-validation
75 / 100 · Review before installing
Check before installing.
By mdbabumiamssm/LLMs-Universal-Life-Science-and-Clinical-Skills- (GitHub) · other · 36 stars · scanned at commit fde6cd1
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 14 places.
Show 11 more
- Skills/Sequence_Analysis/alignment-files/alignment-validation/SKILL.md, line 103
proper=$(samtools view -c -f 2 input.bam) - Skills/Sequence_Analysis/alignment-files/alignment-validation/SKILL.md, line 124
java -jar picard.jar CollectGcBiasMetrics \ - Skills/Sequence_Analysis/alignment-files/alignment-validation/SKILL.md, line 135
computeGCBias \ - Skills/Sequence_Analysis/alignment-files/alignment-validation/SKILL.md, line 158
forward=$(samtools view -c -F 16 input.bam) - Skills/Sequence_Analysis/alignment-files/alignment-validation/SKILL.md, line 169
for chr in chr1 chr2 chr3; do - Skills/Sequence_Analysis/alignment-files/alignment-validation/SKILL.md, line 181
samtools view input.bam | cut -f5 | sort -n | uniq -c | sort -k2 -n - Skills/Sequence_Analysis/alignment-files/alignment-validation/SKILL.md, line 187
samtools view input.bam | awk '{sum+=$5; count++} END {print "Mean MAPQ:", sum/count}' - Skills/Sequence_Analysis/alignment-files/alignment-validation/SKILL.md, line 205
samtools idxstats input.bam | awk '{print $1, $3/$2}' | head -25 - Skills/Sequence_Analysis/alignment-files/alignment-validation/SKILL.md, line 211
samtools idxstats input.bam | awk '$3 > 0 { - Skills/Sequence_Analysis/alignment-files/alignment-validation/SKILL.md, line 229
java -jar picard.jar CollectAlignmentSummaryMetrics \ - Skills/Sequence_Analysis/alignment-files/alignment-validation/SKILL.md, line 248
BAM=$1
Connects to the internet
The author does not mention this.
Found in 8 places.
Show 5 more
- Skills/Sequence_Analysis/alignment-files/alignment-validation/SKILL.md, line 327
for i, read in enumerate(self.bam.fetch()): - Skills/Sequence_Analysis/alignment-files/alignment-validation/examples/validate_alignment.py, line 25
for i, read in enumerate(bam.fetch()): - Skills/Sequence_Analysis/alignment-files/alignment-validation/usage-guide.md, line 198
for i, read in enumerate(bam.fetch()): - Skills/Sequence_Analysis/alignment-files/alignment-validation/usage-guide.md, line 228
for i, read in enumerate(self.bam.fetch()): - Skills/Sequence_Analysis/alignment-files/alignment-validation/usage-guide.md, line 239
for i, read in enumerate(self.bam.fetch()):
Downloads and installs other software
The author does not mention this.
Found in 1 place.
Safer alternatives
Low-risk skills in the same category (other) that look related. Check that one does what you need.
Install
Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.
if [ -e ~/.agents/skills/'alignment-validation' ] || [ -L ~/.agents/skills/'alignment-validation' ]; then echo 'A skill folder named alignment-validation already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/mdbabumiamssm/LLMs-Universal-Life-Science-and-Clinical-Skills-' "$d" && git -C "$d" checkout --quiet 'fde6cd1025d8a9300ad783b3d6696fa708a5cdb0' -- 'Skills/Sequence_Analysis/alignment-files/alignment-validation' && mkdir -p ~/.agents/skills && cp -R "$d"/'Skills/Sequence_Analysis/alignment-files/alignment-validation' ~/.agents/skills/'alignment-validation' && rm -rf "$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/'alignment-validation' ~/.claude/skills/'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.
Badge for your README
The badge for mdbabumiamssm/LLMs-Universal-Life-Science-and-Clinical-Skills- shows the score of its lowest-scoring skill.

[](https://zalavijaysinh.github.io/skilltrust/repos/mdbabumiamssm/LLMs-Universal-Life-Science-and-Clinical-Skills-/)
Score history
| Date | Version | Score |
|---|
| 2026-11-13 | fde6cd1 | 75 |
| 2026-11-07 | 839c35a | 75 |