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long-read-alignment
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 14 places.
Show 11 more
- Skills/Genomics/long-read-sequencing/long-read-alignment/SKILL.md, line 58
minimap2 -d reference.mmi reference.fa - Skills/Genomics/long-read-sequencing/long-read-alignment/SKILL.md, line 67
minimap2 -ax map-ont \ - Skills/Genomics/long-read-sequencing/long-read-alignment/SKILL.md, line 81
minimap2 -ax splice reference.fa reads.fastq.gz | \ - Skills/Genomics/long-read-sequencing/long-read-alignment/SKILL.md, line 89
minimap2 -ax splice --junc-bed junctions.bed \ - Skills/Genomics/long-read-sequencing/long-read-alignment/SKILL.md, line 97
minimap2 -ax asm5 reference.fa assembly.fa > aligned.sam - Skills/Genomics/long-read-sequencing/long-read-alignment/SKILL.md, line 107
minimap2 -x map-ont reference.fa reads.fastq.gz > alignments.paf - Skills/Genomics/long-read-sequencing/long-read-alignment/SKILL.md, line 114
minimap2 -ax map-ont \ - Skills/Genomics/long-read-sequencing/long-read-alignment/SKILL.md, line 124
minimap2 -ax map-ont reference.fa reads.fastq.gz | \ - Skills/Genomics/long-read-sequencing/long-read-alignment/SKILL.md, line 133
minimap2 -ax map-ont reference.fa reads1.fastq.gz reads2.fastq.gz | \ - Skills/Genomics/long-read-sequencing/long-read-alignment/SKILL.md, line 145
samtools flagstat aligned.bam - Skills/Genomics/long-read-sequencing/long-read-alignment/SKILL.md, line 155
awk 'OFS="\t" {print $6, $8, $9, $1, $12, ($5=="+")?"+":"-"}' alignments.paf > alignments.bed
Install
Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.
if [ -e ~/.agents/skills/'long-read-alignment' ] || [ -L ~/.agents/skills/'long-read-alignment' ]; then echo 'A skill folder named long-read-alignment already exists — not replacing it' >&2; false; else d=$(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/Genomics/long-read-sequencing/long-read-alignment' && mkdir -p ~/.agents/skills && cp -R "$d"/'Skills/Genomics/long-read-sequencing/long-read-alignment' ~/.agents/skills/'long-read-alignment' && rm -rf "$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/'long-read-alignment' ~/.claude/skills/'long-read-alignment' (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 | 100 |