Agent skill

Bio Batch Processing

by FreedomIntelligence in FreedomIntelligence/OpenClaw-Medical-Skills

Process multiple sequence files in batch using Biopython. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills.

No licenceAuto-check passedData & Analytics

Install Bio Batch Processing

skills CLI

$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-batch-processing -a claude-code

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

GitHub CLI

$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-batch-processing --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/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/bio-batch-processing .claude/skills/bio-batch-processing && 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-batch-processing" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-batch-processing into .claude/skills/bio-batch-processing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-batch-processing", 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/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-batch-processing

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 FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-batch-processing -a codex

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

GitHub CLI

$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-batch-processing --agent codex

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

Manual copy

$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/bio-batch-processing .agents/skills/bio-batch-processing && 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-batch-processing" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-batch-processing into .agents/skills/bio-batch-processing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-batch-processing", 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 FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-batch-processing -a cursor

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

GitHub CLI

$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-batch-processing --agent cursor

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

Manual copy

$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/bio-batch-processing .cursor/skills/bio-batch-processing && 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-batch-processing" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-batch-processing into .cursor/skills/bio-batch-processing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-batch-processing", 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/FreedomIntelligence/OpenClaw-Medical-Skills.git --path skills/bio-batch-processing

--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 FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-batch-processing -a gemini-cli

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

GitHub CLI

$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-batch-processing --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/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/bio-batch-processing .gemini/skills/bio-batch-processing && 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-batch-processing" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-batch-processing into .gemini/skills/bio-batch-processing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-batch-processing", 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 FreedomIntelligence/OpenClaw-Medical-Skills bio-batch-processing

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 FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-batch-processing -a github-copilot

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

Manual copy

$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/bio-batch-processing .github/skills/bio-batch-processing && 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-batch-processing" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-batch-processing into .github/skills/bio-batch-processing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-batch-processing", 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 FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-batch-processing -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 FreedomIntelligence/OpenClaw-Medical-Skills bio-batch-processing --agent opencode

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

Manual copy

$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/bio-batch-processing .opencode/skills/bio-batch-processing && 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-batch-processing" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-batch-processing into .opencode/skills/bio-batch-processing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-batch-processing", 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-batch-processing
GitHub stars: 3.1k
Used in: 1 other repo
Token cost: ~2.2k tokens
SKILL.md length: 365 words
Files: 3
Skills in repo: 173
Repo updated: Jul 21, 2026
First seen: Oct 7, 2026
Licence: None found

At a glance

Process multiple sequence files in batch using Biopython. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills.

Working with many files
SKILL.md covers Version Compatibility, Required Imports, Process Multiple Files and Merge Files, plus 7 more sections
Runs Python scripts from its folder; calls pip
Merging/splitting sequences

What it does

Bio Batch Processing is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Process multiple sequence files in batch using Biopython. Use when working with many files, merging/splitting sequences, or automating file operations across directories.

Its SKILL.md is about 2.2k tokens, which your agent loads only when the skill is triggered. The skill folder holds 3 other files (for example `examples/batch_process.py` and `usage-guide.md`).

It sits in Data & Analytics, covering Data pipelines and ETL and Bioinformatics. It works with Biopython. The repository describes itself as: The largest open-source medical AI skills library for OpenClaw🦞.

When your agent uses it

Working with many files
Merging/splitting sequences
Automating file operations across directories

Example prompts

“/bio-batch-processing”

Requirements

Python 3

What it can do on your machine

Read from SKILL.md and the folder at commit b1f9b6e. 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
Ships script files (Python), which the agent can run.
Shell commands in SKILL.md call:
- pip
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md. Its commands use pip, which can reach the network depending on how they are called.
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 Batch Processing loads about 2.2k tokens when it runs. Until then it costs about 48 tokens; SKILL.md has 365 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~48
When it runs · the whole SKILL.md, loaded when a task matches: ~2.2k

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

Without a licence we can't republish the file, so here is its outline and opening line. It has 365 words (~2,207 tokens).

“Reference examples tested with: BioPython 1.83+”

— opening of SKILL.md by FreedomIntelligence

name: bio-batch-processing
tool_type: python
primary_tool: Bio.SeqIO

Outline of SKILL.md

Version Compatibility
Batch Processing
Required Imports
Process Multiple Files
Iterate Over Files in Directory
Process All FASTQ Files
Recursive File Search
Merge Files
Merge All FASTA Files
Merge with Source Tracking
Merge Specific Files
Split Files
Split by Number of Records
Split by Sequence ID Prefix
One Sequence Per File
Batch Convert
Convert All Files in Directory
Batch Convert with Summary
Parallel Processing
Using multiprocessing
Using concurrent.futures
Summary Statistics
Aggregate Stats Across Files
Per-File Summary Report
File Organization
Organize by Criteria
Common Patterns
Related Skills

Read the full SKILL.md on GitHub

Files

SKILL.md and 2 other files in skills/bio-batch-processing of FreedomIntelligence/OpenClaw-Medical-Skills.

SKILL.md
examples/batch_process.py
usage-guide.md

Open the folder on GitHubat commit b1f9b6e

Used in 1 other repository

We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in FreedomIntelligence/OpenClaw-Medical-Skills, which our catalogue first saw on October 7, 2026.

BioTender-max/awesome-bio-agent-skillsskills/bioskills/batch-processing

Compare with similar skills

Bio Batch Processing 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 Batch Processing compared with similar skills
Skill	Stars	Used in	Tokens	Auto-check	Licence	Repo updated
Bio Batch Processing this skillFreedomIntelligence/OpenClaw-Medical-Skills	3.1k	1 repos	~2.2k	Automated safety check: Pass	None	2 mo ago
Bio Batch ProcessingGPTomics/bioSkills	1.2k	1 repos	~3k	Automated safety check: Pass	MIT	1 mo ago
GgetK-Dense-AI/scientific-agent-skills	48k	1 repos	~2.8k	Automated safety check: Notes	BSD-2-Clause	2 days ago
Bio Sequence StatisticsGPTomics/bioSkills	1.2k	1 repos	~3.2k	Automated safety check: Pass	MIT	1 mo ago
Biopython Phyloaipoch/medical-research-skills	2k	—	~1.8k	Automated safety check: Pass	MIT	20 days ago
Bio Sequence Statisticsmajiayu000/claude-skill-registry	666	2 repos	~2.1k	Automated safety check: Pass	MIT	today

Similar skills

Bio Batch Processing
GPTomics/bioSkills
Process many sequence files in batch (count, merge, split, convert, summarize) with memory-safe streaming and on-disk indexing using Biopython, pysam, or pyfastx.
1.2k GitHub starsUsed in 1 repo~3k tokens
Data & AnalyticsAuto-check passed
Gget
K-Dense-AI/scientific-agent-skills
Queries 20+ bioinformatics resources through CLI/Python. An agent skill from K-Dense-AI/scientific-agent-skills.
48k GitHub starsUsed in 1 repo~2.8k tokens
Research & ScienceAuto-check: notes
Bio Sequence Statistics
GPTomics/bioSkills
Calculate assembly and sequence statistics (N50/L50, auN, NG50/NGA50, length distribution, GC content with ambiguity handling, summary reports) using Biopython.
1.2k GitHub starsUsed in 1 repo~3.2k tokens
Data & AnalyticsAuto-check passed
Biopython Phylo
aipoch/medical-research-skills
Use Bio.Phylo to read/write phylogenetic trees and perform visualization and statistics; use when tree parsing/conversion, pruning/rerooting, distance calculation, or plotting is required.
2k GitHub stars~1.8k tokensUpdated 20 days ago
Data & AnalyticsAuto-check passed
Bio Sequence Statistics
majiayu000/claude-skill-registry
Calculate sequence statistics (N50, length distribution, GC content, summary reports) using Biopython.
666 GitHub starsUsed in 2 repos~2.1k tokens
Data & AnalyticsAuto-check passed
Bio Restriction Mapping
GPTomics/bioSkills
Build restriction maps showing enzyme cut positions and inter-site distances along DNA using Biopython Bio.Restriction.
1.2k GitHub starsUsed in 1 repo~2.3k tokens
Research & ScienceAuto-check passed

Questions about Bio Batch Processing

What does Bio Batch Processing do?

Process multiple sequence files in batch using Biopython. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Bio Batch Processing is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Process multiple sequence files in batch using Biopython.

When should I use Bio Batch Processing?

Bio Batch Processing fits situations like: working with many files; merging/splitting sequences; automating file operations across directories.

How do I install Bio Batch Processing in Claude Code?

Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-batch-processing -a claude-code`. Or copy the skill folder (skills/bio-batch-processing in FreedomIntelligence/OpenClaw-Medical-Skills) into .claude/skills/bio-batch-processing in your project. Claude Code loads it when a task matches its description.

How do I install Bio Batch Processing in Codex?

Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-batch-processing -a codex`. Or copy the skill folder (skills/bio-batch-processing in FreedomIntelligence/OpenClaw-Medical-Skills) into .agents/skills/bio-batch-processing in your project. Codex loads it when a task matches its description.

Can I use Bio Batch Processing 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 FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-batch-processing -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-batch-processing, .gemini/skills/bio-batch-processing, .github/skills/bio-batch-processing and .opencode/skills/bio-batch-processing in your project.

What does Bio Batch Processing need to run?

Going by SKILL.md and its folder, Bio Batch Processing needs Python for the scripts in its folder and the command-line tools its instructions call (pip). Our summary lists: Python 3.

Does Bio Batch Processing access the network?

SKILL.md contains no URLs. Its commands use pip, which can reach the network depending on how they are called. This is read from the text; nothing was executed.

Is Bio Batch Processing 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 Batch Processing use?

No licence was found for Bio Batch Processing or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.

How many tokens does Bio Batch Processing use?

About 2.2k tokens (SKILL.md is roughly 8.8k 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 Batch Processing?

Skills that share tags, products or a category with Bio Batch Processing: Bio Batch Processing (GPTomics/bioSkills, 1.2k stars), Gget (K-Dense-AI/scientific-agent-skills, 48k stars), Bio Sequence Statistics (GPTomics/bioSkills, 1.2k stars) and Biopython Phylo (aipoch/medical-research-skills, 2k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Bio Batch Processing?

FreedomIntelligence (a GitHub organization) maintains it in FreedomIntelligence/OpenClaw-Medical-Skills, which has 3,051 GitHub stars. The repository holds 173 skills in this directory. The repository was last updated on July 21, 2026.

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

Bio Batch Processing

Install Bio Batch Processing

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

Files

Used in 1 other repository

Compare with similar skills

Similar skills