← All skills
reference-operations
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 19 places.
Show 16 more
- Skills/Sequence_Analysis/alignment-files/reference-operations/SKILL.md, line 51
samtools faidx reference.fa chr1 - Skills/Sequence_Analysis/alignment-files/reference-operations/SKILL.md, line 56
samtools faidx reference.fa chr1:1000-2000 > region.fa - Skills/Sequence_Analysis/alignment-files/reference-operations/SKILL.md, line 61
samtools faidx -i reference.fa chr1:1000-2000 - Skills/Sequence_Analysis/alignment-files/reference-operations/SKILL.md, line 77
samtools dict reference.fa -o reference.dict - Skills/Sequence_Analysis/alignment-files/reference-operations/SKILL.md, line 82
samtools dict -a GRCh38 -s "Homo sapiens" reference.fa -o reference.dict - Skills/Sequence_Analysis/alignment-files/reference-operations/SKILL.md, line 98
samtools consensus input.bam -o consensus.fa - Skills/Sequence_Analysis/alignment-files/reference-operations/SKILL.md, line 103
samtools consensus -r chr1:1000-2000 input.bam -o region_consensus.fa - Skills/Sequence_Analysis/alignment-files/reference-operations/SKILL.md, line 109
samtools consensus -f fasta input.bam -o consensus.fa - Skills/Sequence_Analysis/alignment-files/reference-operations/SKILL.md, line 118
samtools consensus -d 5 input.bam -o consensus.fa - Skills/Sequence_Analysis/alignment-files/reference-operations/SKILL.md, line 127
samtools consensus --show-ins no --show-del no input.bam -o consensus.fa - Skills/Sequence_Analysis/alignment-files/reference-operations/SKILL.md, line 231
samtools faidx reference.fa - Skills/Sequence_Analysis/alignment-files/reference-operations/SKILL.md, line 246
ls -la reference.fa.fai - Skills/Sequence_Analysis/alignment-files/reference-operations/SKILL.md, line 259
samtools faidx reference.fa chr1 > chr1.fa - Skills/Sequence_Analysis/alignment-files/reference-operations/SKILL.md, line 265
cut -f1,2 reference.fa.fai > chrom.sizes - Skills/Sequence_Analysis/alignment-files/reference-operations/SKILL.md, line 270
samtools faidx reference.fa chr1 chr2 chr3 > subset.fa - Skills/Sequence_Analysis/alignment-files/reference-operations/SKILL.md, line 277
samtools consensus input.bam -o consensus.fa
Connects to the internet
The author does not mention this.
Found in 5 places.
Show 2 more
Downloads and installs other software
The author does not mention this.
Found in 1 place.
Install
Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.
if [ -e ~/.agents/skills/'reference-operations' ] || [ -L ~/.agents/skills/'reference-operations' ]; then echo 'A skill folder named reference-operations 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 "$d" checkout --quiet 'fde6cd1025d8a9300ad783b3d6696fa708a5cdb0' -- 'Skills/Sequence_Analysis/alignment-files/reference-operations' && mkdir -p ~/.agents/skills && cp -R "$d"/'Skills/Sequence_Analysis/alignment-files/reference-operations' ~/.agents/skills/'reference-operations' && 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/'reference-operations' ~/.claude/skills/'reference-operations' (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 |