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bismark-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.
What this skill can do
Runs commands on your computer
The author does not mention this.
Found in 14 places.
Show 11 more
- Skills/Epigenomics/methylation-analysis/bismark-alignment/SKILL.md, line 55
bismark --genome /path/to/genome_folder/ \ - Skills/Epigenomics/methylation-analysis/bismark-alignment/SKILL.md, line 69
bismark --genome /path/to/genome_folder/ \ - Skills/Epigenomics/methylation-analysis/bismark-alignment/SKILL.md, line 81
bismark --genome /path/to/genome_folder/ --pbat reads.fastq.gz - Skills/Epigenomics/methylation-analysis/bismark-alignment/SKILL.md, line 88
bismark --genome /path/to/genome_folder/ --non_directional reads.fastq.gz - Skills/Epigenomics/methylation-analysis/bismark-alignment/SKILL.md, line 95
trim_galore --illumina --paired reads_R1.fastq.gz reads_R2.fastq.gz - Skills/Epigenomics/methylation-analysis/bismark-alignment/SKILL.md, line 108
bismark --genome /path/to/genome_folder/ \ - Skills/Epigenomics/methylation-analysis/bismark-alignment/SKILL.md, line 121
cat output_dir/reads_bismark_bt2_SE_report.txt - Skills/Epigenomics/methylation-analysis/bismark-alignment/SKILL.md, line 128
samtools sort output.bam -o output.sorted.bam - Skills/Epigenomics/methylation-analysis/bismark-alignment/SKILL.md, line 136
deduplicate_bismark --bam output_bismark_bt2.bam - Skills/Epigenomics/methylation-analysis/bismark-alignment/SKILL.md, line 146
cat *_SE_report.txt - Skills/Epigenomics/methylation-analysis/bismark-alignment/SKILL.md, line 159
bismark_genome_preparation --hisat2 /path/to/genome_folder/
Install
Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.
if [ -e ~/.agents/skills/'bismark-alignment' ] || [ -L ~/.agents/skills/'bismark-alignment' ]; then echo 'A skill folder named bismark-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 "$d" checkout --quiet 'fde6cd1025d8a9300ad783b3d6696fa708a5cdb0' -- 'Skills/Epigenomics/methylation-analysis/bismark-alignment' && mkdir -p ~/.agents/skills && cp -R "$d"/'Skills/Epigenomics/methylation-analysis/bismark-alignment' ~/.agents/skills/'bismark-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/'bismark-alignment' ~/.claude/skills/'bismark-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 | 95 |