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alignment-sorting
82 / 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.
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 24 places.
Show 17 more
- Skills/Sequence_Analysis/alignment-files/alignment-sorting/SKILL.md, line 56
samtools sort -m 4G -@ 4 -o sorted.bam input.bam - Skills/Sequence_Analysis/alignment-files/alignment-sorting/SKILL.md, line 61
samtools sort -T /tmp/sort_tmp -o sorted.bam input.bam - Skills/Sequence_Analysis/alignment-files/alignment-sorting/SKILL.md, line 67
samtools sort -O bam -o sorted.bam input.bam - Skills/Sequence_Analysis/alignment-files/alignment-sorting/SKILL.md, line 76
samtools sort -t CB -o sorted_by_barcode.bam input.bam - Skills/Sequence_Analysis/alignment-files/alignment-sorting/SKILL.md, line 81
bwa mem ref.fa reads.fq | samtools sort -o aligned.bam - Skills/Sequence_Analysis/alignment-files/alignment-sorting/SKILL.md, line 90
samtools collate -o collated.bam input.bam - Skills/Sequence_Analysis/alignment-files/alignment-sorting/SKILL.md, line 103
samtools view -H input.bam | grep "^@HD" - Skills/Sequence_Analysis/alignment-files/alignment-sorting/SKILL.md, line 112
samtools view input.bam | awk '$4 < prev {exit 1} {prev=$4}' - Skills/Sequence_Analysis/alignment-files/alignment-sorting/SKILL.md, line 164
subprocess.run( - Skills/Sequence_Analysis/alignment-files/alignment-sorting/SKILL.md, line 166
shell=True, check=True - Skills/Sequence_Analysis/alignment-files/alignment-sorting/SKILL.md, line 178
aligner = subprocess.Popen(['bwa', 'mem', 'ref.fa', 'reads.fq'], - Skills/Sequence_Analysis/alignment-files/alignment-sorting/SKILL.md, line 192
samtools merge merged.bam sample1.bam sample2.bam sample3.bam - Skills/Sequence_Analysis/alignment-files/alignment-sorting/SKILL.md, line 197
samtools merge -@ 4 merged.bam sample1.bam sample2.bam sample3.bam - Skills/Sequence_Analysis/alignment-files/alignment-sorting/SKILL.md, line 203
samtools merge -b files.txt merged.bam - Skills/Sequence_Analysis/alignment-files/alignment-sorting/SKILL.md, line 208
samtools merge -f merged.bam sample1.bam sample2.bam - Skills/Sequence_Analysis/alignment-files/alignment-sorting/SKILL.md, line 213
samtools merge -R chr1:1000000-2000000 merged_region.bam sample1.bam sample2.bam - Skills/Sequence_Analysis/alignment-files/alignment-sorting/SKILL.md, line 227
bwa mem -t 8 ref.fa R1.fq R2.fq | samtools sort -@ 4 -o aligned.bam
and 4 more places
Downloads and installs other software
The author does not mention this.
Found in 1 place.
Install
Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.
if [ -e ~/.agents/skills/'alignment-sorting' ] || [ -L ~/.agents/skills/'alignment-sorting' ]; then echo 'A skill folder named alignment-sorting already exists — not replacing it' >&2; false; else d=$(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-sorting' && mkdir -p ~/.agents/skills && cp -R "$d"/'Skills/Sequence_Analysis/alignment-files/alignment-sorting' ~/.agents/skills/'alignment-sorting' && rm -rf "$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-sorting' ~/.claude/skills/'alignment-sorting' (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 | 82 |
| 2026-11-07 | 839c35a | 82 |