Agent skill

Bio Tools

Bioinformatics workflow guide for sequence analysis, QC, plotting, structure rendering, and literature search.

Apache-2.0Auto-check passedResearch & Science

Install Bio Tools

skills CLI

$ npx skills add DrugClaw/DrugClaw --skill bio-tools -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI

$ gh skill install DrugClaw/DrugClaw bio-tools --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy

$ git clone --depth 1 https://github.com/DrugClaw/DrugClaw.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/science/bio-tools .claude/skills/bio-tools && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Paste into Claude Code

Install the "bio-tools" agent skill from https://github.com/DrugClaw/DrugClaw/tree/main/skills/science/bio-tools into .claude/skills/bio-tools/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-tools", then confirm the skill loads.

Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

$skill-installer

$skill-installer install https://github.com/DrugClaw/DrugClaw/tree/main/skills/science/bio-tools

Type this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.

skills CLI

$ npx skills add DrugClaw/DrugClaw --skill bio-tools -a codex

Project install goes to .agents/skills/; add -g for ~/.codex/skills/.

GitHub CLI

$ gh skill install DrugClaw/DrugClaw bio-tools --agent codex

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/DrugClaw/DrugClaw.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/science/bio-tools .agents/skills/bio-tools && rm -rf skills-src

Use ~/.agents/skills/ instead of .agents/skills for a personal install.

Codex skills documentation · loads skills from .agents/skills/

Paste into Codex

Install the "bio-tools" agent skill from https://github.com/DrugClaw/DrugClaw/tree/main/skills/science/bio-tools into .agents/skills/bio-tools/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-tools", then confirm the skill loads.

Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add DrugClaw/DrugClaw --skill bio-tools -a cursor

Project install goes to .agents/skills/; add -g for ~/.cursor/skills/.

GitHub CLI

$ gh skill install DrugClaw/DrugClaw bio-tools --agent cursor

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/DrugClaw/DrugClaw.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/science/bio-tools .cursor/skills/bio-tools && rm -rf skills-src

Use ~/.cursor/skills/ instead of .cursor/skills for a personal install.

Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/

Paste into Cursor

Install the "bio-tools" agent skill from https://github.com/DrugClaw/DrugClaw/tree/main/skills/science/bio-tools into .cursor/skills/bio-tools/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-tools", then confirm the skill loads.

Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

gemini skills install

$ gemini skills install https://github.com/DrugClaw/DrugClaw.git --path skills/science/bio-tools

--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.

skills CLI

$ npx skills add DrugClaw/DrugClaw --skill bio-tools -a gemini-cli

Project install goes to .agents/skills/; add -g for ~/.gemini/skills/.

GitHub CLI

$ gh skill install DrugClaw/DrugClaw bio-tools --agent gemini-cli

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/DrugClaw/DrugClaw.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/science/bio-tools .gemini/skills/bio-tools && rm -rf skills-src

Use ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.

Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/

Paste into Gemini CLI

Install the "bio-tools" agent skill from https://github.com/DrugClaw/DrugClaw/tree/main/skills/science/bio-tools into .gemini/skills/bio-tools/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-tools", then confirm the skill loads.

Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

GitHub CLI

$ gh skill install DrugClaw/DrugClaw bio-tools

Installs for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).

skills CLI

$ npx skills add DrugClaw/DrugClaw --skill bio-tools -a github-copilot

Project install goes to .agents/skills/; add -g for ~/.copilot/skills/.

Manual copy

$ git clone --depth 1 https://github.com/DrugClaw/DrugClaw.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/science/bio-tools .github/skills/bio-tools && rm -rf skills-src

Use ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.

GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/

Paste into GitHub Copilot

Install the "bio-tools" agent skill from https://github.com/DrugClaw/DrugClaw/tree/main/skills/science/bio-tools into .github/skills/bio-tools/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-tools", then confirm the skill loads.

GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add DrugClaw/DrugClaw --skill bio-tools -a opencode

OpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.

GitHub CLI

$ gh skill install DrugClaw/DrugClaw bio-tools --agent opencode

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/DrugClaw/DrugClaw.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/science/bio-tools .opencode/skills/bio-tools && rm -rf skills-src

Use ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.

OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/

Paste into OpenCode

Install the "bio-tools" agent skill from https://github.com/DrugClaw/DrugClaw/tree/main/skills/science/bio-tools into .opencode/skills/bio-tools/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-tools", then confirm the skill loads.

OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

Facts

Skill name: bio-tools
GitHub stars: 125
Token cost: ~1.9k tokens
SKILL.md length: 425 words
Files: 1
Skills in repo: 25
Repo updated: Mar 23, 2026
First seen: Oct 7, 2026
Licence: Apache-2.0

At a glance

Bioinformatics workflow guide for sequence analysis, QC, plotting, structure rendering, and literature search.

Works in 6 steps: Inspect available inputs. → Identify data type: FASTA, FASTQ, BAM,… → Check tool availability. → …
Tasks that involve Bioinformatics
SKILL.md covers Environment Check, Working Style, Common Workflow and File Triage, plus 9 more sections
Calls python3 and curl; reaches files.rcsb.org

What it does

Bio Tools is an agent skill from DrugClaw/DrugClaw. Bioinformatics workflow guide for sequence analysis, QC, plotting, structure rendering, and literature search.

Its SKILL.md is about 1.9k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.

It sits in Research & Science, covering Bioinformatics, Literature review and Data visualization. The repository describes itself as: 💊 AI Research Assistant for Accelerated Drug Discovery. 🦞. The licence is Apache-2.0.

When your agent uses it

Tasks that involve Bioinformatics
Tasks that involve Literature review
Tasks that involve Data visualization

Example prompts

“Use the bio-tools skill to bioinformatic workflow guide for sequence analysis, QC, plotting, structure rendering, and literature search”
“/bio-tools”

Requirements

Python 3

Workflow steps

6 steps, taken from the first numbered list in SKILL.md.

Inspect available inputs.
Identify data type: FASTA, FASTQ, BAM, BED, CSV/TSV, PDB, SMILES, etc.
Check tool availability.
Run the smallest validating command first.
Save primary outputs and a short README or command log when analysis is non-trivial.
Summarize findings with caveats and suggested follow-ups.

What it can do on your machine

Read from SKILL.md and the folder at commit 960a6e0. It shows what the files ask for, not the result of running them.

Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Shell commands in SKILL.md call:
- python3
- curl
From the folder's file list and the shell code blocks in SKILL.md.
Network
Hosts in commands or code, which the agent is likely to contact:
- files.rcsb.org
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Bio Tools loads about 1.9k tokens when it runs. Until then it costs about 30 tokens; SKILL.md has 425 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~30
When it runs · the whole SKILL.md, loaded when a task matches: ~1.9k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from DrugClaw/DrugClaw at commit 960a6e0, republished under its Apache-2.0 licence (© DrugClaw). 425 words, ~1,884 tokens.

Download SKILL.mdSave it as .claude/skills/bio-tools/SKILL.md (or your agent's skills folder).

name: bio-tools
description: Bioinformatics workflow guide for sequence analysis, QC, plotting, structure rendering, and literature search.
source: drugclaw
updated_at: 2026-03-10

Bio Tools

Use this skill for bioinformatics, genomics, transcriptomics, structural biology, or general biological data-analysis requests.

This skill focuses on DrugClaw's reproducible bioinformatics workflow pattern:

Run commands with bash
Write reproducible scripts with write_file or edit_file
Inspect outputs with read_file
Use web_search / web_fetch for literature and database lookups

Environment Check

Do not assume the runtime already has the biology stack. Check first.

bash

which python3 blastn blastp samtools bedtools bwa minimap2 fastqc seqtk pymol || true
python3 - <<'PY'
mods = ["Bio", "pandas", "numpy", "matplotlib", "pysam", "seaborn", "sklearn"]
for name in mods:
    try:
        __import__(name)
        print(f"{name}: ok")
    except Exception as exc:
        print(f"{name}: missing ({exc})")
PY

If key tools are missing, say so explicitly and recommend the optional drug-sandbox image documented in docs/operations/science-runtime.md.

Working Style

Start by inventorying files and formats in the current chat working directory.
State the exact command, parameters, and tool versions used.
Save outputs as files in the working directory and mention their paths in the reply.
Prefer reproducible scripts over one-off interactive commands for multi-step analysis.
Flag quality issues, contamination risk, reference mismatch, and missing metadata.
End with concrete next steps, not just raw output.

Common Workflow

Inspect available inputs.
Identify data type: FASTA, FASTQ, BAM, BED, CSV/TSV, PDB, SMILES, etc.
Check tool availability.
Run the smallest validating command first.
Save primary outputs and a short README or command log when analysis is non-trivial.
Summarize findings with caveats and suggested follow-ups.

File Triage

bash

pwd
find . -maxdepth 3 -type f | sort
file sample.fastq.gz
gzip -dc sample.fastq.gz | head

Useful quick checks:

bash

samtools --version | head -n 1
blastn -version
fastqc --version
python3 --version

Sequence Search

bash

# Nucleotide BLAST against a local FASTA database
blastn -query query.fa -subject reference.fa -outfmt 6 -evalue 1e-5 > blast.tsv

# Protein BLAST
blastp -query protein.fa -subject reference_proteins.fa -outfmt 6 > blastp.tsv

# Translate nucleotide query against proteins
blastx -query transcript.fa -subject proteins.fa -outfmt 6 > blastx.tsv

For remote NCBI lookups, prefer Python so the workflow is easy to archive:

python

from Bio import Entrez, SeqIO

Entrez.email = "research@example.com"
handle = Entrez.efetch(db="nucleotide", id="NM_000546", rettype="fasta", retmode="text")
record = SeqIO.read(handle, "fasta")
print(record.id, len(record.seq))

Read Alignment And BAM Processing

bash

# Build index
bwa index reference.fa

# Short-read alignment
bwa mem reference.fa reads_R1.fastq.gz reads_R2.fastq.gz > aligned.sam

# Long-read alignment
minimap2 -a reference.fa long_reads.fastq.gz > aligned.sam

# SAM -> sorted/indexed BAM
samtools view -bS aligned.sam | samtools sort -o aligned.sorted.bam
samtools index aligned.sorted.bam
samtools flagstat aligned.sorted.bam > aligned.flagstat.txt

FASTQ Quality Control

bash

mkdir -p qc
fastqc reads_R1.fastq.gz reads_R2.fastq.gz -o qc

# Quick sequence statistics
seqtk comp reads_R1.fastq.gz | head
seqtk size reads_R1.fastq.gz

Report at minimum:

total reads
adapter or overrepresented sequence warnings
per-base quality drop-off
GC bias
whether trimming/filtering is needed before alignment

Genome Arithmetic

bash

bedtools intersect -a peaks.bed -b genes.bed > overlap.bed
bedtools coverage -a targets.bed -b aligned.sorted.bam > coverage.tsv
bedtools getfasta -fi reference.fa -bed targets.bed > targets.fa

Python Analysis Recipes

Sequence I/O

python

from Bio import SeqIO

for record in SeqIO.parse("input.fa", "fasta"):
    print(record.id, len(record.seq))

Show full SKILL.md (171 more words)Show less

Differential Expression

python

import pandas as pd
from pydeseq2.dds import DeseqDataSet
from pydeseq2.ds import DeseqStats

counts = pd.read_csv("counts.csv", index_col=0)
meta = pd.read_csv("metadata.csv", index_col=0)

dds = DeseqDataSet(counts=counts, metadata=meta, design="~condition")
dds.deseq2()
stats = DeseqStats(dds, contrast=["condition", "treated", "control"])
stats.summary()
res = stats.results_df.sort_values("padj")
res.to_csv("deseq2_results.csv")

Single-Cell RNA-seq

python

import scanpy as sc

adata = sc.read_h5ad("data.h5ad")
sc.pp.normalize_total(adata)
sc.pp.log1p(adata)
sc.pp.highly_variable_genes(adata)
sc.pp.pca(adata)
sc.pp.neighbors(adata)
sc.tl.umap(adata)
sc.tl.leiden(adata)
sc.pl.umap(adata, color="leiden", save="_leiden.png")

Publication-Style Plots

python

import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns

df = pd.read_csv("expression.csv")
sns.set_theme(style="whitegrid")
ax = sns.scatterplot(data=df, x="log2FoldChange", y="-log10_padj", hue="significant")
ax.figure.savefig("volcano.png", dpi=300, bbox_inches="tight")

Structural Biology

Fetch structures from PDB with web_fetch or direct download, then render with PyMOL if available.

bash

curl -L https://files.rcsb.org/download/1M17.pdb -o 1M17.pdb
cat > render.pml <<'PML'
load 1M17.pdb, prot
hide everything
show cartoon, prot
spectrum count, rainbow, prot
bg_color white
png 1M17_rainbow.png, width=1600, height=1200, dpi=200, ray=1
quit
PML
pymol -cq render.pml

When PyMOL is unavailable, still provide the fetched structure, any residue/chain findings, and the exact rendering script the user can run later.

Literature Search

Use web_search or PubMed APIs for recent papers. For structured PubMed workflows:

python

from Bio import Entrez

Entrez.email = "research@example.com"
search = Entrez.esearch(db="pubmed", term="CRISPR off-target 2025[dp]", retmax=5)
ids = Entrez.read(search)["IdList"]
summary = Entrez.esummary(db="pubmed", id=",".join(ids))
print(Entrez.read(summary))

Summaries should include:

citation
study type
model system
main finding
why it matters for the user's question

Outputs

Good replies should mention:

what inputs were used
what commands/scripts were run
what files were generated
the most important biological conclusion
uncertainty or validation limits

Example closing pattern:

text

I aligned the reads against GRCh38 with bwa mem and generated `aligned.sorted.bam` plus `aligned.flagstat.txt`.
FastQC shows 3' quality decay after cycle 125 and adapter contamination in R2, so trimming before re-alignment is recommended.
Next step: run fastp or cutadapt, then repeat alignment and variant calling.

For remote biology database lookups across UniProt, PDB, AlphaFold, ClinVar, Ensembl, GEO, InterPro, KEGG, OpenTargets, Reactome, or STRING, activate bio-db-tools. For AnnData, single-cell dataset profiling, alignment-region inspection, or mzML inventory, activate omics-tools. For public drug-discovery database lookups across PubChem, ChEMBL, openFDA, ClinicalTrials.gov, or OpenAlex, activate pharma-db-tools. For molecular docking or pose inspection, activate docking-tools. For DeepChem, PySCF, RDKit descriptors, or chemistry-specific follow-up, activate chem-tools.

Files

Just SKILL.md in skills/science/bio-tools of DrugClaw/DrugClaw.

Open the folder on GitHubat commit 960a6e0

Compare with similar skills

Bio Tools next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Bio Tools compared with similar skills
Skill	Stars	Used in	Tokens	Auto-check	Licence	Repo updated
Bio Tools this skillDrugClaw/DrugClaw	125	—	~1.9k	Automated safety check: Pass	Apache-2.0	6 mo ago
Outline AgentAr9av/PaperOrchestra	677	1 repos	~1.6k	Automated safety check: Pass	Custom licence	18 days ago
Paper OrchestraAr9av/PaperOrchestra	677	1 repos	~3.5k	Automated safety check: Pass	Custom licence	18 days ago
Plotting AgentAr9av/PaperOrchestra	677	1 repos	~2.3k	Automated safety check: Pass	Custom licence	18 days ago
Scanpy Single-Cell Analysisdavila7/claude-code-templates	32k	15 repos	~2.8k	Automated safety check: Pass	MIT	yesterday
deepTools NGS Toolkitdavila7/claude-code-templates	32k	12 repos	~4.5k	Automated safety check: Pass	MIT	yesterday

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Questions about Bio Tools

What does Bio Tools do?

Bioinformatics workflow guide for sequence analysis, QC, plotting, structure rendering, and literature search. Bio Tools is an agent skill from DrugClaw/DrugClaw. Bioinformatics workflow guide for sequence analysis, QC, plotting, structure rendering, and literature search.

When should I use Bio Tools?

Bio Tools fits situations like: tasks that involve Bioinformatics; tasks that involve Literature review; tasks that involve Data visualization.

How do I install Bio Tools in Claude Code?

Run `npx skills add DrugClaw/DrugClaw --skill bio-tools -a claude-code`. Or copy the skill folder (skills/science/bio-tools in DrugClaw/DrugClaw) into .claude/skills/bio-tools in your project. Claude Code loads it when a task matches its description.

How do I install Bio Tools in Codex?

Run `npx skills add DrugClaw/DrugClaw --skill bio-tools -a codex`. Or copy the skill folder (skills/science/bio-tools in DrugClaw/DrugClaw) into .agents/skills/bio-tools in your project. Codex loads it when a task matches its description.

Can I use Bio Tools in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add DrugClaw/DrugClaw --skill bio-tools -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/bio-tools, .gemini/skills/bio-tools, .github/skills/bio-tools and .opencode/skills/bio-tools in your project.

What does Bio Tools need to run?

Going by SKILL.md and its folder, Bio Tools needs the command-line tools its instructions call (python3 and curl). Our summary lists: Python 3.

Does Bio Tools access the network?

SKILL.md names 1 domain. In commands or code: files.rcsb.org; the agent is likely to contact it when it follows the instructions. This is read from the text; nothing was executed.

Is Bio Tools safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Bio Tools use?

Bio Tools is published under the Apache-2.0 licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Bio Tools use?

About 1.9k tokens (SKILL.md is roughly 7.5k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Bio Tools?

Skills that share tags, products or a category with Bio Tools: Outline Agent (Ar9av/PaperOrchestra, 677 stars), Paper Orchestra (Ar9av/PaperOrchestra, 677 stars), Plotting Agent (Ar9av/PaperOrchestra, 677 stars) and Scanpy Single-Cell Analysis (davila7/claude-code-templates, 32k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Bio Tools?

DrugClaw (a GitHub organization) maintains it in DrugClaw/DrugClaw, which has 125 GitHub stars. The repository holds 25 skills in this directory. The repository was last updated on March 23, 2026.

Source: DrugClaw/DrugClaw on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.

Install Bio Tools

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

Workflow steps

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

Bio Tools

Environment Check

Working Style

Common Workflow

File Triage

Sequence Search

Read Alignment And BAM Processing

FASTQ Quality Control

Genome Arithmetic

Python Analysis Recipes

Sequence I/O

Differential Expression

Single-Cell RNA-seq

Publication-Style Plots

Structural Biology

Literature Search

Outputs

Related Skill

Files

Compare with similar skills

Similar skills

More from DrugClaw/DrugClaw

Related

Questions about Bio Tools