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bio-reference-operations
90 / 100 · Low risk
Fine to try.
By BioTender-max/awesome-bio-agent-skills (GitHub) · design · 219 stars · scanned at commit 8cbdd18
Generate consensus sequences and manage reference files using samtools. Use when creating consensus from alignments, indexing references, or creating sequence dictionaries.
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 22 places.
Show 17 more
- skills/bioskills/reference-operations/SKILL.md, line 53
samtools faidx reference.fa chr1 - skills/bioskills/reference-operations/SKILL.md, line 58
samtools faidx reference.fa chr1:1000-2000 > region.fa - skills/bioskills/reference-operations/SKILL.md, line 63
samtools faidx -i reference.fa chr1:1000-2000 - skills/bioskills/reference-operations/SKILL.md, line 79
samtools dict reference.fa -o reference.dict - skills/bioskills/reference-operations/SKILL.md, line 84
samtools dict -a GRCh38 -s "Homo sapiens" reference.fa -o reference.dict - skills/bioskills/reference-operations/SKILL.md, line 118
samtools view -H sample.bam | grep '^@SQ' | head -3 - skills/bioskills/reference-operations/SKILL.md, line 130
samtools consensus input.bam -o consensus.fa - skills/bioskills/reference-operations/SKILL.md, line 135
samtools consensus -r chr1:1000-2000 input.bam -o region_consensus.fa - skills/bioskills/reference-operations/SKILL.md, line 141
samtools consensus -f fasta input.bam -o consensus.fa - skills/bioskills/reference-operations/SKILL.md, line 150
samtools consensus -d 5 input.bam -o consensus.fa - skills/bioskills/reference-operations/SKILL.md, line 160
samtools consensus --ambig --het-fract 0.2 --call-fract 0.5 input.bam -o consensus.fa - skills/bioskills/reference-operations/SKILL.md, line 168
samtools consensus -f fasta input.bam -o consensus.fa - skills/bioskills/reference-operations/SKILL.md, line 192
samtools consensus --config illumina -d 10 --het-fract 0.5 \ - skills/bioskills/reference-operations/SKILL.md, line 306
samtools faidx reference.fa - skills/bioskills/reference-operations/SKILL.md, line 320
ls -la reference.fa.fai - skills/bioskills/reference-operations/SKILL.md, line 333
samtools faidx reference.fa chr1 > chr1.fa - skills/bioskills/reference-operations/SKILL.md, line 339
cut -f1,2 reference.fa.fai > chrom.sizes
and 2 more places
Connects to the internet
The author does not mention this.
Found in 2 places.
Install
Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.
if [ -e ~/.agents/skills/'bio-reference-operations' ] || [ -L ~/.agents/skills/'bio-reference-operations' ]; then echo 'A skill folder named bio-reference-operations already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/BioTender-max/awesome-bio-agent-skills' "$d" && git -C "$d" checkout --quiet '8cbdd18837aa6296c4e77616a03b323bd69b57b1' -- 'skills/bioskills/reference-operations' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bioskills/reference-operations' ~/.agents/skills/'bio-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/'bio-reference-operations' ~/.claude/skills/'bio-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 BioTender-max/awesome-bio-agent-skills shows the score of its lowest-scoring skill.
[](https://zalavijaysinh.github.io/skilltrust/repos/BioTender-max/awesome-bio-agent-skills/)
Score history
| Date | Version | Score |
|---|
| 2026-11-07 | 8cbdd18 | 75 |