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duplicate-handling
95 / 100 · Low risk
Fine to try.
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.
Partially scanned — some files couldn't be read; we'll retry on the next scan
What this skill can do
Runs commands on your computer
The author does not mention this.
Found in 18 places.
Show 15 more
- Skills/Sequence_Analysis/alignment-files/duplicate-handling/SKILL.md, line 81
samtools fixmate -m namesorted.bam fixmate.bam - Skills/Sequence_Analysis/alignment-files/duplicate-handling/SKILL.md, line 86
samtools fixmate -m -@ 4 namesorted.bam fixmate.bam - Skills/Sequence_Analysis/alignment-files/duplicate-handling/SKILL.md, line 91
samtools fixmate -r -m namesorted.bam fixmate.bam - Skills/Sequence_Analysis/alignment-files/duplicate-handling/SKILL.md, line 100
samtools markdup input.bam marked.bam - Skills/Sequence_Analysis/alignment-files/duplicate-handling/SKILL.md, line 105
samtools markdup -r input.bam deduped.bam - Skills/Sequence_Analysis/alignment-files/duplicate-handling/SKILL.md, line 110
samtools markdup -s input.bam marked.bam 2> markdup_stats.txt - Skills/Sequence_Analysis/alignment-files/duplicate-handling/SKILL.md, line 116
samtools markdup -d 2500 input.bam marked.bam - Skills/Sequence_Analysis/alignment-files/duplicate-handling/SKILL.md, line 121
samtools markdup -@ 4 input.bam marked.bam - Skills/Sequence_Analysis/alignment-files/duplicate-handling/SKILL.md, line 126
samtools markdup -f stats.txt input.bam marked.bam - Skills/Sequence_Analysis/alignment-files/duplicate-handling/SKILL.md, line 133
samtools flagstat marked.bam - Skills/Sequence_Analysis/alignment-files/duplicate-handling/SKILL.md, line 140
samtools view -c -f 1024 marked.bam - Skills/Sequence_Analysis/alignment-files/duplicate-handling/SKILL.md, line 145
total=$(samtools view -c marked.bam) - Skills/Sequence_Analysis/alignment-files/duplicate-handling/SKILL.md, line 234
bwa-mem2 mem ref.fa R1.fq R2.fq | \ - Skills/Sequence_Analysis/alignment-files/duplicate-handling/SKILL.md, line 241
java -jar picard.jar MarkDuplicates \ - Skills/Sequence_Analysis/alignment-files/duplicate-handling/SKILL.md, line 267
samtools view -f 1024 marked.bam
Install
Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.
if [ -e ~/.agents/skills/'duplicate-handling' ] || [ -L ~/.agents/skills/'duplicate-handling' ]; then echo 'A skill folder named duplicate-handling already exists — not replacing it' >&2; false; else d=$(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/duplicate-handling' && mkdir -p ~/.agents/skills && cp -R "$d"/'Skills/Sequence_Analysis/alignment-files/duplicate-handling' ~/.agents/skills/'duplicate-handling' && rm -rf "$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/'duplicate-handling' ~/.claude/skills/'duplicate-handling' (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 | 95 |
| 2026-11-07 | 839c35a | 80 |